dputhier / pygtftk Goto Github PK

A python package and a set of shell commands to handle GTF files

License: GNU General Public License v3.0

Makefile 0.75% Python 82.03% Shell 0.15% R 0.07% C 11.43% Dockerfile 0.01% C++ 0.72% Cython 4.84%

bioinformatics gene gtf bed bigwig genomics transcript exon cds genomic

pygtftk's Introduction

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Python GTF toolkit (pygtftk)

The Python GTF toolkit (pygtftk) package is intended to ease handling of GTF/GFF2.0 files (Gene Transfer Format). It currently does not support GFF3 file format. The pygtftk package is compatible with Python 3.9 and relies on libgtftk, a library of functions written in C.

The package comes with a set of UNIX commands that can be accessed through the gtftk program. The gtftk program proposes several atomic tools to filter, convert, or extract data from GTF files.

The newly released command, OLOGRAM (OverLap Of Genomic Regions Analysis using Monte Carlo) may be used to compute overlap statistics between user supplied regions (BED format) and annotation derived from :

Gene centric features enclosed in a GTF (e.g. exons, promoters, terminators...).
Regions in a GTFs flagged with built-in keys/values (e.g. check the 'gene_biotype' as provided by ensembl GTFs of the regions in which peaks fall).
Same with custom keys/values through the gtftk CLI (e.g. adding a numeric value to a gene and discretizing this value to create gene classes).
User supplied BED files.

With the most recent update, OLOGRAM is now also capable of computing the enrichment of n-wise combinations (ie. A+B, A+B+C, etc.) to find correlation groups of regions. Please see the documentation page of OLOGRAM for more details.

The gtftk set of Unix commands can be easily extended using a basic plugin architecture.

All these aspects are covered in the help sections ; please see the documentation.

While the gtftk Unix program comes with hundreds of unitary and functional tests, it is still in active development and may thus suffer from bugs that remain to be discovered. Feel free to post any problem or required enhancement in the issue section of the GitHub repository.

Documentation

Documentation about the latest release is available as a github page.

Documentation about OLOGRAM (OverLap Of Genomic Regions Analysis using Monte Carlo) can be found in the 'ologram' section of the documentation.

NB: The readthedoc version won't be maintained and will be closed in the near future. This choice was motivated by the impossibility to maintain a dynamic documentation (using sphinx/sphinxcontrib-programoutput) given the computing time provided by readthedoc server.

Note that example dataset are available to test the various subcommands (see documentation page).

gtftk get_example -h # E.g. to get all file from the 'simple' dataset gtftk get_example -d simple -f "*"

System requirements

Depending on the size of the GTF file, pygtftk and gtftk may require lot of memory to perform selected tasks. A computer with 16Go is recommended in order to be able to pipe several commands when working with human annotations from ensembl release (e.g. 91). When working with a cluster think about reserving sufficient memory.

At the moment, the gtftk program has been tested on:

Linux (Ubuntu 12.04 and 18.04)

OSX (Yosemite, El Capitan, Mojave).

Installation

Installation through conda package building

Installation through conda should be the preferred install solution. The pygtftk package and gtftk command line tool require external dependencies (bedtools ">v2.23.1", graphviz, unzip) with some version constrains.

If conda is not available on your system, first install miniconda from the official web site and make sure you have bioconda and conda-forge channels set up in the order below.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then you can simply install pygtftk in its own isolated environment and activate it.

conda create -n pygtftk pygtftk
conda activate pygtftk

Installation through setup.py

This is not the preferred way for installation. Choose conda whenever possible. We have observed several issues with dependencies that still need to be fixed.

git clone http://[email protected]:dputhier/pygtftk.git pygtftk
cd pygtftk
# Check your Python version (>=3.8,<3.9)
pip install -r requirements.txt
python setup.py install

Installation through pip

Prerequisites

Again, this is not the preferred way for installation. Please choose conda whenever possible. We have observed several issues with dependencies that still need to be fixed.

Running pip

Installation through pip can be done as follow.

pip install -r requirements.txt
pip install pygtftk
# It is important to call gtftk -h
# to look for plugins and their
# CLI in ~/.gtftk
# before going further
gtftk -h

Testing

Running functional tests

A lot of functional tests have been developed to ensure consistency with expected results. This does not rule out that bugs may hide throughout the code... In order to check that installation is functional you may be interested in running functional tests. The definition of all functional tests declared in gtftk commands is accessible using the -p/--plugin-tests argument:

gtftk -p

To run the tests, you will need to install bats (Bash Automated Testing System). Once bats is installed run the following commands:

# The tests should be run in the pygtftk git
# directory because several tests contains references (relative path)
# to file enclosed in pygtftk/data directory.
gtftk -p > gtftk_test.bats
bats gtftk_test.bats

Note, alternatively you may directly call the tests using the Makefile.

make clean
make test

Or run tests in parallel using:

make clean
make test_para -j 10 # Using 10 cores

Running unitary tests

Several unitary tests have been implemented using doctests. You can run them using nose through the following command line:

make nose

pygtftk's People

Contributors

Stargazers

Watchers

Forkers

stefanucci-luca cgnat embl-hentze-group tqh003 ouertani95 yuanmaosen

pygtftk's Issues

get_tx_seq: should accept genome in gz format without complaining.

Morever the GlobbedFileList action does not throw error when file does not exist nor complain if the extension is the wrong one.

.gtftk versioning

It could be interesting to allow several subdirectories in .gtftk (that would be named according to a hash computed from the path to the gtftk script). The idea would be to avoid collisions between several versions of pygtftk (e.g installed through several envs) with potentially various plugins.

Improving the detection/annotation of alternative splicing events

It would be interesting to create plugins to detect the various spicing events described in Hadas Keren, Galit Lev-Maor & Gil Ast (Alternative splicing and evolution: diversification, exon definition and function).

http://www.nature.com.gate2.inist.fr/nrg/journal/v11/n5/box/nrg2776_BX1.html

peak_anno: "frequencies has a zero element at %s." % (zeropos,)) ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).

Hi,
When running peak_anno with example files (containing only features on chr1) and full chromosome table/size, peak_anno crash:

  gtftk peak_anno -i pygtftk/data/mini_real/mini_real.gtf.gz -o toto -c pygtftk/data/mini_real/hg38.genome -p pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -V 3
   |-- 11:27:24-INFO-peak_anno : Checking chromosome info file.
   |-- 11:27:24-INFO-peak_anno : Instantiating a GTF.
   |-- 11:27:25-DEBUG-peak_anno : Calling extract_data_iter.
   |-- 11:27:25-DEBUG-peak_anno : Ensembl format detected.
   |-- 11:27:25-DEBUG_MEM-peak_anno : GTF created  (#l=137670, p=0x7fc53fbd1110, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808999288, n=1).
   |-- 11:27:25-DEBUG-peak_anno : Calling select_by_key (key=seqid, value=chr1,chr2,chr3,chr4...)
   |-- 11:27:25-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
   |-- 11:27:25-INFO-peak_anno : Instantiating a GTF.
   |-- 11:27:25-DEBUG_MEM-peak_anno : GTF created  (#l=137670, p=0x7fc54737f530, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808971736, n=2).
   |-- 11:27:25-DEBUG_MEM-peak_anno : GTF deleted  (#l=137670, p=0x7fc53fbd1110, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808999288, n=1).
   |-- 11:27:25-DEBUG-peak_anno : Calling 'get_chroms'.
   |-- 11:27:25-DEBUG-peak_anno : Calling 'get_feature_list'.
   |-- 11:27:25-DEBUG-peak_anno : Calling extract_data (feature).
   |-- 11:27:26-DEBUG-peak_anno : Calling select_by_key (key=feature, value=gene)
   |-- 11:27:26-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
   |-- 11:27:26-INFO-peak_anno : Instantiating a GTF.
   |-- 11:27:26-DEBUG_MEM-peak_anno : GTF created  (#l=1058, p=0x7fc52d9cac80, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808693152, n=3).
   |-- 11:27:26-DEBUG-peak_anno : Calling 'to_bed' method.
   |-- 11:27:26-DEBUG-peak_anno : Calling extract_data (seqid,start,end,score,strand,transcript_id,gene_id,exon_id).
   |-- 11:27:26-DEBUG_MEM-peak_anno : GTF deleted  (#l=1058, p=0x7fc52d9cac80, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808693152, n=3).
   |-- 11:27:26-INFO-peak_anno : Beginning shuffling for a given set of features...
   |-- 11:27:26-DEBUG-peak_anno : BATCHES : 10 batches of 20 shuffles
   |-- 11:27:26-DEBUG-peak_anno : Total number of shuffles : 200
   |-- 11:27:26-DEBUG-peak_anno : NB_THREADS = 8
   |-- 11:27:26-DEBUG-peak_anno : BED files read as lists of intervals in 0.17975282669067383 s
   |-- 11:27:26-INFO-peak_anno : --- Minibatch nb. : 1 / 10
   |-- 11:27:26-DEBUG-peak_anno : Batch generated and shuffled in 0.023317813873291016 s
   |-- 11:27:26-DEBUG-peak_anno : Batch converted to fake beds in : 0.1311180591583252 s
   |-- 11:27:27-DEBUG-peak_anno : All intersections computed by custom code in : 0.6467368602752686 s
   |-- 11:27:27-INFO-peak_anno : --- Minibatch nb. : 2 / 10
   |-- 11:27:27-DEBUG-peak_anno : Batch generated and shuffled in 0.019360065460205078 s
   |-- 11:27:27-DEBUG-peak_anno : Batch converted to fake beds in : 0.12729096412658691 s
   |-- 11:27:28-DEBUG-peak_anno : All intersections computed by custom code in : 0.6355540752410889 s
   |-- 11:27:28-INFO-peak_anno : --- Minibatch nb. : 3 / 10
   |-- 11:27:28-DEBUG-peak_anno : Batch generated and shuffled in 0.018916845321655273 s
   |-- 11:27:28-DEBUG-peak_anno : Batch converted to fake beds in : 0.13068914413452148 s
   |-- 11:27:28-DEBUG-peak_anno : All intersections computed by custom code in : 0.6408717632293701 s
   |-- 11:27:28-INFO-peak_anno : --- Minibatch nb. : 4 / 10
   |-- 11:27:28-DEBUG-peak_anno : Batch generated and shuffled in 0.0192258358001709 s
   |-- 11:27:29-DEBUG-peak_anno : Batch converted to fake beds in : 0.12983202934265137 s
   |-- 11:27:29-DEBUG-peak_anno : All intersections computed by custom code in : 0.6501920223236084 s
   |-- 11:27:29-INFO-peak_anno : --- Minibatch nb. : 5 / 10
   |-- 11:27:29-DEBUG-peak_anno : Batch generated and shuffled in 0.0198819637298584 s
   |-- 11:27:29-DEBUG-peak_anno : Batch converted to fake beds in : 0.13089895248413086 s
   |-- 11:27:30-DEBUG-peak_anno : All intersections computed by custom code in : 0.7375490665435791 s
   |-- 11:27:30-INFO-peak_anno : --- Minibatch nb. : 6 / 10
   |-- 11:27:30-DEBUG-peak_anno : Batch generated and shuffled in 0.020968914031982422 s
   |-- 11:27:30-DEBUG-peak_anno : Batch converted to fake beds in : 0.1310739517211914 s
   |-- 11:27:31-DEBUG-peak_anno : All intersections computed by custom code in : 0.7431747913360596 s
   |-- 11:27:31-INFO-peak_anno : --- Minibatch nb. : 7 / 10
   |-- 11:27:31-DEBUG-peak_anno : Batch generated and shuffled in 0.01874995231628418 s
   |-- 11:27:31-DEBUG-peak_anno : Batch converted to fake beds in : 0.1322779655456543 s
   |-- 11:27:32-DEBUG-peak_anno : All intersections computed by custom code in : 0.6475603580474854 s
   |-- 11:27:32-INFO-peak_anno : --- Minibatch nb. : 8 / 10
   |-- 11:27:32-DEBUG-peak_anno : Batch generated and shuffled in 0.0187680721282959 s
   |-- 11:27:32-DEBUG-peak_anno : Batch converted to fake beds in : 0.12628579139709473 s
   |-- 11:27:33-DEBUG-peak_anno : All intersections computed by custom code in : 0.7448949813842773 s
   |-- 11:27:33-INFO-peak_anno : --- Minibatch nb. : 9 / 10
   |-- 11:27:33-DEBUG-peak_anno : Batch generated and shuffled in 0.019285917282104492 s
   |-- 11:27:33-DEBUG-peak_anno : Batch converted to fake beds in : 0.13170504570007324 s
   |-- 11:27:34-DEBUG-peak_anno : All intersections computed by custom code in : 0.7476060390472412 s
   |-- 11:27:34-INFO-peak_anno : --- Minibatch nb. : 10 / 10
   |-- 11:27:34-DEBUG-peak_anno : Batch generated and shuffled in 0.018893003463745117 s
   |-- 11:27:34-DEBUG-peak_anno : Batch converted to fake beds in : 0.12927627563476562 s
   |-- 11:27:35-DEBUG-peak_anno : All intersections computed by custom code in : 0.7500202655792236 s
   |-- 11:27:35-DEBUG-peak_anno : All intersections have been generated.
   |-- 11:27:35-DEBUG-peak_anno : Statistics on overlaps computed in : 0.12702703475952148 s
  Traceback (most recent call last):
    File "/Users/puthier/miniconda3/envs/pygtftk/bin/gtftk", line 4, in <module>
      __import__('pkg_resources').run_script('pygtftk==0.9.9.dev0+cbb3', 'gtftk')
    File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 661, in run_script
      self.require(requires)[0].run_script(script_name, ns)
    File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1441, in run_script
      exec(code, namespace, namespace)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 104, in <module>
      args = main()
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 89, in main
      CmdManager.run(args)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/cmd_manager.py", line 950, in run
      fun(**args)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/plugins/peak_anno.py", line 457, in peak_anno
      hits[feat_type] = overlap_partial(bedA=peak_file, bedB=gtf_sub_bed)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/overlap_stats_shuffling.py", line 229, in compute_overlap_stats
      ps = nf.check_negbin_adjustment(summed_bp_overlaps, esperance_fitted_summed_bp_overlaps, variance_fitted_summed_bp_overlaps)#.pvalue
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 90, in check_negbin_adjustment
      result = 1 - cramers_V(crosstab)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 84, in cramers_V
      chi2 = scipy.stats.chi2_contingency(crosstab)[0]
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/scipy/stats/contingency.py", line 253, in chi2_contingency
      "frequencies has a zero element at %s." % (zeropos,))
  ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).
   |-- 11:27:44-DEBUG_MEM-peak_anno : GTF deleted  (#l=0, p=0x7fc54737f530, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120808971736, n=2).
   puthier  (pygtftk) 
    peak_anno_shuffling ● ? ⍟5  …/pygtftk  gtftk peak_anno -i pygtftk/data/mini_real/mini_real.gtf.gz -o toto -c pygtftk/data/mini_real/hg38.genome -p pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -V 3
                                                                                $RPROMPT_PREFIX$(build_right_prompt)$reset_color$RPROMPT_SUFFIX
   puthier  (pygtftk) 
    peak_anno_shuffling ● ? ⍟5  …/pygtftk  gunzip -c pygtftk/data/mini_real/mini_real.gtf.gz| less  1 ↵  ⚙  10067  11:28:07
   puthier  (pygtftk) 
    peak_anno_shuffling ● ? ⍟5  …/pygtftk  less pygtftk/data/mini_real/hg38.genome        PIPE(-13)|0 ↵  ⚙  10068  11:28:16
   puthier  (pygtftk) 
    peak_anno_shuffling ● ? ⍟5  …/pygtftk  cp pygtftk/data/mini_real/hg38.genome hg38                 ✔  ⚙  10069  11:28:26
   puthier  (pygtftk) 
    peak_anno_shuffling ● ? ⍟5  …/pygtftk  gtftk peak_anno -i pygtftk/data/mini_real/mini_real.gtf.gz -o toto -c hg38  -p pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -V 3
   |-- 11:28:53-INFO-peak_anno : Checking chromosome info file.
   |-- 11:28:53-INFO-peak_anno : Instantiating a GTF.
   |-- 11:28:53-DEBUG-peak_anno : Calling extract_data_iter.
   |-- 11:28:53-DEBUG-peak_anno : Ensembl format detected.
   |-- 11:28:53-DEBUG_MEM-peak_anno : GTF created  (#l=137670, p=0x7fb5380d4010, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752028752, n=1).
   |-- 11:28:53-DEBUG-peak_anno : Calling select_by_key (key=seqid, value=chr1,chr2,chr3,chr4...)
   |-- 11:28:54-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
   |-- 11:28:54-INFO-peak_anno : Instantiating a GTF.
   |-- 11:28:54-DEBUG_MEM-peak_anno : GTF created  (#l=137670, p=0x7fb5380e3840, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752000528, n=2).
   |-- 11:28:54-DEBUG_MEM-peak_anno : GTF deleted  (#l=137670, p=0x7fb5380d4010, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752028752, n=1).
   |-- 11:28:54-DEBUG-peak_anno : Calling 'get_chroms'.
   |-- 11:28:54-DEBUG-peak_anno : Calling 'get_feature_list'.
   |-- 11:28:54-DEBUG-peak_anno : Calling extract_data (feature).
   |-- 11:28:55-DEBUG-peak_anno : Calling select_by_key (key=feature, value=gene)
   |-- 11:28:55-INFO-peak_anno : Found file pygtftk/data/mini_real/mini_real.gtf.gz
   |-- 11:28:55-INFO-peak_anno : Instantiating a GTF.
   |-- 11:28:55-DEBUG_MEM-peak_anno : GTF created  (#l=1058, p=0x7fb5380d7eb0, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120751718296, n=3).
   |-- 11:28:55-DEBUG-peak_anno : Calling 'to_bed' method.
   |-- 11:28:55-DEBUG-peak_anno : Calling extract_data (seqid,start,end,score,strand,transcript_id,gene_id,exon_id).
   |-- 11:28:55-DEBUG_MEM-peak_anno : GTF deleted  (#l=0, p=0x7fb5380d7eb0, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120751718296, n=3).
   |-- 11:28:55-INFO-peak_anno : Beginning shuffling for a given set of features...
   |-- 11:28:55-DEBUG-peak_anno : BATCHES : 10 batches of 20 shuffles
   |-- 11:28:55-DEBUG-peak_anno : Total number of shuffles : 200
   |-- 11:28:55-DEBUG-peak_anno : NB_THREADS = 8
   |-- 11:28:55-DEBUG-peak_anno : BED files read as lists of intervals in 0.15019702911376953 s
   |-- 11:28:55-INFO-peak_anno : --- Minibatch nb. : 1 / 10
   |-- 11:28:55-DEBUG-peak_anno : Batch generated and shuffled in 0.018970966339111328 s
   |-- 11:28:55-DEBUG-peak_anno : Batch converted to fake beds in : 0.13421201705932617 s
   |-- 11:28:56-DEBUG-peak_anno : All intersections computed by custom code in : 0.6478052139282227 s
   |-- 11:28:56-INFO-peak_anno : --- Minibatch nb. : 2 / 10
   |-- 11:28:56-DEBUG-peak_anno : Batch generated and shuffled in 0.01854705810546875 s
   |-- 11:28:56-DEBUG-peak_anno : Batch converted to fake beds in : 0.1281449794769287 s
   |-- 11:28:56-DEBUG-peak_anno : All intersections computed by custom code in : 0.6428921222686768 s
   |-- 11:28:56-INFO-peak_anno : --- Minibatch nb. : 3 / 10
   |-- 11:28:56-DEBUG-peak_anno : Batch generated and shuffled in 0.01955699920654297 s
   |-- 11:28:57-DEBUG-peak_anno : Batch converted to fake beds in : 0.13239288330078125 s
   |-- 11:28:57-DEBUG-peak_anno : All intersections computed by custom code in : 0.6378078460693359 s
   |-- 11:28:57-INFO-peak_anno : --- Minibatch nb. : 4 / 10
   |-- 11:28:57-DEBUG-peak_anno : Batch generated and shuffled in 0.01935100555419922 s
   |-- 11:28:57-DEBUG-peak_anno : Batch converted to fake beds in : 0.1293799877166748 s
   |-- 11:28:58-DEBUG-peak_anno : All intersections computed by custom code in : 0.6441848278045654 s
   |-- 11:28:58-INFO-peak_anno : --- Minibatch nb. : 5 / 10
   |-- 11:28:58-DEBUG-peak_anno : Batch generated and shuffled in 0.018750905990600586 s
   |-- 11:28:58-DEBUG-peak_anno : Batch converted to fake beds in : 0.1291358470916748 s
   |-- 11:28:59-DEBUG-peak_anno : All intersections computed by custom code in : 0.6483819484710693 s
   |-- 11:28:59-INFO-peak_anno : --- Minibatch nb. : 6 / 10
   |-- 11:28:59-DEBUG-peak_anno : Batch generated and shuffled in 0.019301176071166992 s
   |-- 11:28:59-DEBUG-peak_anno : Batch converted to fake beds in : 0.13379311561584473 s
   |-- 11:29:00-DEBUG-peak_anno : All intersections computed by custom code in : 0.6421530246734619 s
   |-- 11:29:00-INFO-peak_anno : --- Minibatch nb. : 7 / 10
   |-- 11:29:00-DEBUG-peak_anno : Batch generated and shuffled in 0.018435001373291016 s
   |-- 11:29:00-DEBUG-peak_anno : Batch converted to fake beds in : 0.1339731216430664 s
   |-- 11:29:00-DEBUG-peak_anno : All intersections computed by custom code in : 0.7524068355560303 s
   |-- 11:29:00-INFO-peak_anno : --- Minibatch nb. : 8 / 10
   |-- 11:29:01-DEBUG-peak_anno : Batch generated and shuffled in 0.018976926803588867 s
   |-- 11:29:01-DEBUG-peak_anno : Batch converted to fake beds in : 0.13104987144470215 s
   |-- 11:29:01-DEBUG-peak_anno : All intersections computed by custom code in : 0.7570860385894775 s
   |-- 11:29:01-INFO-peak_anno : --- Minibatch nb. : 9 / 10
   |-- 11:29:01-DEBUG-peak_anno : Batch generated and shuffled in 0.01871800422668457 s
   |-- 11:29:02-DEBUG-peak_anno : Batch converted to fake beds in : 0.1300792694091797 s
   |-- 11:29:02-DEBUG-peak_anno : All intersections computed by custom code in : 0.7510981559753418 s
   |-- 11:29:02-INFO-peak_anno : --- Minibatch nb. : 10 / 10
   |-- 11:29:02-DEBUG-peak_anno : Batch generated and shuffled in 0.018780946731567383 s
   |-- 11:29:02-DEBUG-peak_anno : Batch converted to fake beds in : 0.1317291259765625 s
   |-- 11:29:03-DEBUG-peak_anno : All intersections computed by custom code in : 0.7473132610321045 s
   |-- 11:29:03-DEBUG-peak_anno : All intersections have been generated.
   |-- 11:29:03-DEBUG-peak_anno : Statistics on overlaps computed in : 0.1287541389465332 s
  Traceback (most recent call last):
    File "/Users/puthier/miniconda3/envs/pygtftk/bin/gtftk", line 4, in <module>
      __import__('pkg_resources').run_script('pygtftk==0.9.9.dev0+cbb3', 'gtftk')
    File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 661, in run_script
      self.require(requires)[0].run_script(script_name, ns)
    File "/Users/puthier/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1441, in run_script
      exec(code, namespace, namespace)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 104, in <module>
      args = main()
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/EGG-INFO/scripts/gtftk", line 89, in main
      CmdManager.run(args)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/cmd_manager.py", line 950, in run
      fun(**args)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/plugins/peak_anno.py", line 457, in peak_anno
      hits[feat_type] = overlap_partial(bedA=peak_file, bedB=gtf_sub_bed)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/overlap_stats_shuffling.py", line 229, in compute_overlap_stats
      ps = nf.check_negbin_adjustment(summed_bp_overlaps, esperance_fitted_summed_bp_overlaps, variance_fitted_summed_bp_overlaps)#.pvalue
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 90, in check_negbin_adjustment
      result = 1 - cramers_V(crosstab)
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/pygtftk-0.9.9.dev0+cbb3-py3.6-macosx-10.7-x86_64.egg/pygtftk/stats/intersect/negbin_fit.py", line 84, in cramers_V
      chi2 = scipy.stats.chi2_contingency(crosstab)[0]
    File "/Users/puthier/miniconda3/envs/pygtftk/lib/python3.6/site-packages/scipy/stats/contingency.py", line 253, in chi2_contingency
      "frequencies has a zero element at %s." % (zeropos,))
  ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).
   |-- 11:29:13-DEBUG_MEM-peak_anno : GTF deleted  (#l=137670, p=0x7fb5380e3840, f=pygtftk/data/mini_real/mini_real.gtf.gz, i=120752000528, n=2).

Code improvement

In line 312 in Line.py, a While loop should be used instead of the ugly:

        for k, v in zip(ptr.attributes.attr[0:self.nb_key], ptr.attributes.attr[0:self.nb_key]):
            self.attr[ffi.string(k.key).decode()] = ffi.string(v.value).decode()

split command

Could be helpful to have a split command.

e.g

gtftk split -k gene_biotype
gtftk split -k chrom

Blast output to GTF

It could be interesting to propose a blast to gff/gtf output as required in this post on biostar:
https://www.biostars.org/p/277/

Setup.py could contain an extra_require slot in setup()

As an example:

setup(
    name="my_package",
    # (...)
    install_requires=[
        'requests',
        'simplejson'],
    extras_require={
        'tests': [
            'nose',
            'pycodestyle >= 2.1.0'],
        'docs': [
            'sphinx >= 1.4',
            'sphinx_rtd_theme']}
)

Check whether -C is supported with 'retrieve'

Bad extension check for outfile in gtftk coverage

It seems that new version of gtftk coverage expects outfile to be a bw whereas it can be a tabulated matrix with --matrix-out.

gtftk coverage            --inputfile out/bedtools/merge/bedtools/multiinter_bed-hg38-bs-hypometh-thymus/multiinter.bed            --outfile out/gtftk/coverage_chrominfo-hg38-main-chr_upstream-2000_downstream-2000_pseudocount-0_nbwindow-20_nhighest-5_matrixout_bed-hg38-bs-hypometh-thymus-union-all_bw-hg38-H3K27ac-thymus-merged-wiq.txt            --chrom-info out/awk/extract_main_chr/gunzip/to-stdout/rsync/ucsc/goldenPath/hg38/database/chromInfo.txt            --nb-proc 1            --nb-window 20 --matrix-out --upstream 2000 --downstream 2000 --pseudo-count 0 --n-highest 5            out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/CD34_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/EC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/LC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP4_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP8_qnorVS_SP8.bw
    |--- 23:50-WARNING : Not a valid filename extension
    |--- 23:50-ERROR : Extension expected: ('\\.[Bb][Ww]$', '\\.[Bb][Ii][Gg][Ww][Ii][Gg]$')

Redirecting through stdout avoid extension check and the output file seems to be correct.

gtftk coverage            --inputfile out/bedtools/merge/bedtools/multiinter_bed-hg38-bs-hypometh-thymus/multiinter.bed                    --chrom-info out/awk/extract_main_chr/gunzip/to-stdout/rsync/ucsc/goldenPath/hg38/database/chromInfo.txt            --nb-proc 1            --nb-window 20 --matrix-out --upstream 2000 --downstream 2000 --pseudo-count 0 --n-highest 5            out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/CD34_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/EC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/LC_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP4_qnorVS_SP8.bw out/ucsc/wigToBigWig_hg38_clip/danpos/wiq_hg38/danpos/dtriple_width-10_distance-100_edge-1_paired-0/ln/alias/experiments/hg38_H3K27ac_thymus/SP8_qnorVS_SP8.bw > debug.txt

Conda dist of pygtftk not available under OSX

One of the main developpers is working under OSX :).

libgtftk.so compilation

from fafa: The pb with compilation of library is still there. When you do a "file" on the library compiled with gtftk installation, you get : Mach-O 64-bit bundle x86_64
The same "file" on the library I compiled by hand ( gcc -o libgtftk.so -fPIC -shared -lz -I. .c command/.c ) give : Mach-O 64-bit dynamically linked shared library x86_64
The right options (-dynamiclib -shared) appears on the compilation lines but not on the link line, when you link together all the compiled files to build the library. It is probably needed to add these options elsewhere in the config file to tell the linker to make a dynamically linked shared library instead of a bundle.

Add a command-wise argument to convert (chr)MT into (chr)M

This is in progress and will be part of the next libgtftk release.

Some temporary files are left

The worker_coverage_* files are not added to pygtftk.utils.TMP_FILE_LIST. Most likely due to some concurrency issues when using pool.

get_tx_seq sequence truncated.

In version 0.9.8 get_tx_seq do not return properly the sequence. It seems that most sequences on minus strand are truncated. This was not highlighted by tests that, in this case, use short artificial transcripts. This should be fixed and new tests added.

Completion not working under zsh

See the title... No idea at the moment...

retrieve usage in interpreter

When using retrieve inside an interpreter, setting the output file name to the expected one (i.e. name of the downloaded file from ftp) result in no download. This may be due to 'ftp.download_if_newer()' on line 264 of retrieve.py.

 import pygtftk.utils
 from  pygtftk.utils import get_example_file
 from tempfile import NamedTemporaryFile
 from pygtftk.gtf_interface import GTF
 from pygtftk.plugins.retrieve import retrieve
 retrieve(species_name='homo_sapiens', release='91',    outputfile=open('Homo_sapiens.GRCh38.91.chr.gtf.gz', 'w')
...: )

select_by_key should throw an error when no key/val is available.

Example:
gtftk join_attr -i simple.gtf -j simple.join_mat -k gene_id -V 2 -m -t exon | gtftk select_by_key

compatible python3

The pygtftk library should be compatible with Py3k.

Distutils package at installation - 'ftputils'

During installation with the pip install pygtftk command, an error occurs when trying to uninstall ftputils 3.2, presumably to install a pygtftk-compatible version :

"Cannot uninstall 'ftputil'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall."

Workaround : calling the installation with pip install --ignore-installed pygtftk results in pip skipping the package and installing correctly pygtftk, but this is not a viable solution as it will lead to older packages being kept and could result in a dependency error.

For test reproducibility chrom_info_as_dict should use an OrderedDict instead of a defaultDict

TODO

ArgFormatter.bed6

Instead of screaming when provided a bed3 file, bed6 should instead automatically convert it to bed6 and display a warning for the user.

Adding test to check wether bigwigs contain the expected chrs

bw = pyBigWig.open("test/test.bw")
bw.chroms().keys()

gtftk retrieve -c and -o should be mutually exclusive

Todo.

ERROR-mk_matrix with conda packaged version of release 0.9.1

The first conda package for pygtftk is out:
https://anaconda.org/guillaumecharbonnier/pygtftk
I am not able to pass tests requiring this file though:
ERROR-mk_matrix : Not a bigwig file :pygtftk/data/simple/simple.bw

Maybe an issue with the version of pyBigWig?

            bigwig = pyBigWig.open(big_wig)
            if not bigwig.isBigWig():
                message("Not a bigwig file :" + big_wig, type="ERROR")

Version of pybigwig in packaged environment:
https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.2.8-py27_0.tar.bz2

Version of pybigwig in working unpackaged environment:
https://conda.anaconda.org/bioconda/linux-64/pybigwig-0.3.10-np113py27_0.tar.bz2

Currently rebuilding with higher-version requirement to see if it solves the issue.

peak_anno error upon installation

Got an error during installation of pygtftk (related to cythonization of create_shuffle)

  pygtftk/stats/intersect/create_shuffles.c:626:10: fatal error: 'numpy/arrayobject.h' file not found
  #include "numpy/arrayobject.h"
           ^
  1 error generated.
  error: command 'clang' failed with exit status 1

hide_undef is not supported by extract_data when a TAB object is returned

import pygtftk.utils
from  pygtftk.utils import get_example_file
from tempfile import NamedTemporaryFile
from pygtftk.gtf_interface import GTF
a_file = get_example_file()[0]
gtf = GTF("Homo_sapiens.GRCh38.91.chr.gtf.gz")
a = gtf.extract_data("start,end,transcript_id", hide_undef=True)

Not meaningful

Closed

force-tx-class is not supported in profile

Loosen dep requirements

issue with select_by_regexp

The command uses re.match. It should use re.search. Will be fixed in the next release.

argformatter: bed6 and FileWithExtension should be merge

Both should be merged into a single class/action

 file_format(mode='r', file_ext='bed')

Closest_gn_to_feat

In case sloped regions exceed genome size the computed distance to the features going outside genome limits could be wrong. Should be extremely rare but should be fixed.

Some functions use mutable arguments as default arg

Harmful. Should be fixed.

Exit code 247 on readthedoc

I had recurrent issues with building on readthedoc with an exit code 247. I managed to fix it in commit 6e8439c by deleting some conda channels. This could maybe help others in the future...

Example file

Ensure all tests are not related to any directory.

divergent / convergent list of transcript

In the current implementation only a single transcript is added in the "divergent" key. The list of all of them should be returned.

check self.dict upon deletion of an attribute

Upon gtf.del_attr(...) the corresponding key should be deleted from self.dict and GTF._instance_attr.
To be checked.

Hardcoded gcc at some point in setup.py?

I have been trying for a few days to build pygtftk using bioconda guidelines.
I am not sure about what I am saying but I think that it is failing until now because "gcc" is called somewhere in the install script and the bioconda building environment does not have "gcc". Instead it modifies CC and other C-related variables like this:

echo $CC
 /opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc

For the first part of setup.py, everything is fine because compilations are using the "conda gcc":

/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/blast_reader.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared

But then, after a few ones, "gcc" is used instead and fail because it corresponds to nothing in the environment:

gcc -pthread -shared -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_to_pos.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_blast.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/merge_attr.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_positions.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_transcript.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_exon_number.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_prefix.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/libgtftk.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_raw_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_gtf_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_number_of_exon.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/convert_to_ensembl.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/extract_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_genomic_location.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/clear_indexes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_list.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_key.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_sequences.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/globals.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/del_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_gtf.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/gtf_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_transcript_size.o -L/usr/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -lz -lpython3.6m -o build/lib.linux-x86_64-3.6/pygtftk/lib/libgtftk.cpython-36m-x86_64-linux-gnu.so

@dputhier, do you know how to patch setup.py to always use gcc in CC?

Here is the full log:

No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Adding in variants from /opt/conda/conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /opt/conda/conda_build_config.yaml
Adding in variants from /root/project/recipes/pygtftk/conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /root/project/recipes/pygtftk/conda_build_config.yaml
Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
Attempting to finalize metadata for pygtftk
INFO:conda_build.metadata:Attempting to finalize metadata for pygtftk
Solving environment: ...working... done
Solving environment: ...working... done
Solving environment: ...working... done
BUILD START: ['pygtftk-0.9.7-py36hebb334c_1.tar.bz2']
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place


The following NEW packages will be INSTALLED:

    argparse:             1.4.0-py36_0                         bioconda   
    asn1crypto:           0.24.0-py36_1003                     conda-forge
    bcftools:             1.9-h4da6232_0                       bioconda   
    bedtools:             2.27.1-he941832_2                    bioconda   
    biopython:            1.72-py36_0                          conda-forge
    blas:                 1.1-openblas                         conda-forge
    boost-cpp:            1.67.0-h3a22d5f_0                    conda-forge
    bzip2:                1.0.6-h470a237_2                     conda-forge
    ca-certificates:      2018.8.24-ha4d7672_0                 conda-forge
    cairo:                1.14.12-he6fea26_5                   conda-forge
    certifi:              2018.8.24-py36_1001                  conda-forge
    cffi:                 1.11.5-py36h5e8e0c9_1                conda-forge
    chardet:              3.0.4-py36_1003                      conda-forge
    click:                7.0-py_0                             conda-forge
    click-plugins:        1.0.4-py_0                           conda-forge
    cligj:                0.5.0-py_0                           conda-forge
    cloudpickle:          0.6.0-py_0                           conda-forge
    cryptography:         2.3.1-py36hdffb7b8_0                 conda-forge
    cryptography-vectors: 2.3.1-py36_1000                      conda-forge
    curl:                 7.61.1-h74213dd_2                    conda-forge
    cycler:               0.10.0-py_1                          conda-forge
    cython:               0.28.5-py36hfc679d8_0                conda-forge
    dbus:                 1.13.0-h3a4f0e9_0                    conda-forge
    descartes:            1.1.0-py_2                           conda-forge
    expat:                2.2.5-hfc679d8_2                     conda-forge
    fiona:                1.7.13-py36hb00a9d7_3                conda-forge
    fontconfig:           2.13.1-h65d0f4c_0                    conda-forge
    freetype:             2.9.1-h6debe1e_4                     conda-forge
    freexl:               1.0.5-h470a237_2                     conda-forge
    ftputil:              3.4-py_0                             conda-forge
    future:               0.16.0-py36_1002                     conda-forge
    gdal:                 2.2.4-py36hb00a9d7_9                 conda-forge
    geopandas:            0.4.0-py_1                           conda-forge
    geos:                 3.6.2-hfc679d8_3                     conda-forge
    geotiff:              1.4.2-h700e5ad_4                     conda-forge
    gettext:              0.19.8.1-h5e8e0c9_1                  conda-forge
    giflib:               5.1.4-h470a237_1                     conda-forge
    glib:                 2.55.0-h464dc38_2                    conda-forge
    gst-plugins-base:     1.12.5-hde13a9d_0                    conda-forge
    gstreamer:            1.12.5-h61a6719_0                    conda-forge
    hdf4:                 4.2.13-h951d187_2                    conda-forge
    hdf5:                 1.10.2-hc401514_2                    conda-forge
    htslib:               1.9-hc238db4_4                       bioconda   
    icu:                  58.2-hfc679d8_0                      conda-forge
    idna:                 2.7-py36_1002                        conda-forge
    jpeg:                 9c-h470a237_1                        conda-forge
    json-c:               0.12.1-h470a237_1                    conda-forge
    kealib:               1.4.9-h0bee7d0_2                     conda-forge
    kiwisolver:           1.0.1-py36h2d50403_2                 conda-forge
    krb5:                 1.16.1-hbb41f41_0                    conda-forge
    libcurl:              7.61.1-hbdb9355_2                    conda-forge
    libdap4:              3.19.1-h8fe5423_1                    conda-forge
    libdeflate:           1.0-h470a237_0                       bioconda   
    libedit:              3.1.20170329-haf1bffa_1              conda-forge
    libffi:               3.2.1-hfc679d8_5                     conda-forge
    libgcc-ng:            8.2.0-hdf63c60_1                     defaults   
    libgdal:              2.2.4-hbd6f514_9                     conda-forge
    libgfortran:          3.0.0-1                              conda-forge
    libiconv:             1.15-h470a237_3                      conda-forge
    libkml:               1.3.0-hccc92b1_8                     conda-forge
    libnetcdf:            4.6.1-he6cff42_8                     conda-forge
    libpng:               1.6.35-ha92aebf_2                    conda-forge
    libpq:                10.5-he29860b_0                      conda-forge
    libspatialindex:      1.8.5-hfc679d8_3                     conda-forge
    libspatialite:        4.3.0a-hdfcc80b_23                   conda-forge
    libssh2:              1.8.0-h5b517e9_2                     conda-forge
    libstdcxx-ng:         7.2.0-hdf63c60_3                     conda-forge
    libtiff:              4.0.9-he6b73bb_2                     conda-forge
    libuuid:              2.32.1-h470a237_2                    conda-forge
    libxcb:               1.13-h470a237_2                      conda-forge
    libxml2:              2.9.8-h422b904_5                     conda-forge
    matplotlib:           2.2.3-py36h8e2386c_0                 conda-forge
    mizani:               0.4.6-py_0                           conda-forge
    munch:                2.3.2-py_0                           conda-forge
    ncurses:              6.1-hfc679d8_1                       conda-forge
    numpy:                1.9.3-py36_blas_openblashd3ea46f_206 conda-forge [blas_openblas]
    openblas:             0.2.20-8                             conda-forge
    openjpeg:             2.3.0-h0e734dc_3                     conda-forge
    openssl:              1.0.2p-h470a237_0                    conda-forge
    palettable:           3.1.1-py_0                           conda-forge
    pandas:               0.23.4-py36hf8a1672_0                conda-forge
    patsy:                0.5.0-py_1                           conda-forge
    pcre:                 8.41-hfc679d8_3                      conda-forge
    pip:                  18.1-py36_1000                       conda-forge
    pixman:               0.34.0-h470a237_3                    conda-forge
    plotnine:             0.4.0-py_0                           conda-forge
    poppler:              0.67.0-h4d7e492_3                    conda-forge
    poppler-data:         0.4.9-0                              conda-forge
    postgresql:           10.5-h66035e0_0                      conda-forge
    proj4:                4.9.3-h470a237_8                     conda-forge
    psycopg2:             2.7.5-py36hdffb7b8_2                 conda-forge
    pthread-stubs:        0.4-h470a237_1                       conda-forge
    pybedtools:           0.7.10-py36ha92aebf_3                bioconda   
    pybigwig:             0.3.12-py36hdfb72b2_0                bioconda   
    pycparser:            2.19-py_0                            conda-forge
    pyopenssl:            18.0.0-py36_1000                     conda-forge
    pyparsing:            2.2.2-py_0                           conda-forge
    pyproj:               1.9.5.1-py36h508ed2a_5               conda-forge
    pyqt:                 5.6.0-py36h8210e8a_7                 conda-forge
    pysal:                1.14.4.post2-py36_1                  conda-forge
    pysam:                0.15.1-py36h0380709_0                bioconda   
    pysocks:              1.6.8-py36_1002                      conda-forge
    python:               3.6.6-h5001a0f_0                     conda-forge
    python-dateutil:      2.7.3-py_0                           conda-forge
    pytz:                 2018.5-py_0                          conda-forge
    pyyaml:               3.13-py36h470a237_1                  conda-forge
    qt:                   5.6.2-hf70d934_9                     conda-forge
    readline:             7.0-haf1bffa_1                       conda-forge
    requests:             2.19.1-py36_1001                     conda-forge
    rtree:                0.8.3-py36_1000                      conda-forge
    samtools:             1.9-h8ee4bcc_1                       bioconda   
    scipy:                1.1.0-py36_blas_openblashd3ea46f_201 conda-forge [blas_openblas]
    setuptools:           40.4.3-py36_0                        conda-forge
    shapely:              1.6.4-py36h164cb2d_1                 conda-forge
    sip:                  4.18.1-py36hfc679d8_0                conda-forge
    six:                  1.11.0-py36_1001                     conda-forge
    sqlalchemy:           1.2.12-py36h470a237_0                conda-forge
    sqlite:               3.25.2-hb1c47c0_0                    conda-forge
    statsmodels:          0.9.0-py36h3010b51_0                 defaults   
    tk:                   8.6.8-ha92aebf_0                     conda-forge
    tornado:              5.1.1-py36h470a237_0                 conda-forge
    urllib3:              1.23-py36_1001                       conda-forge
    wheel:                0.32.1-py36_0                        conda-forge
    xerces-c:             3.2.0-h5d6a6da_2                     conda-forge
    xorg-kbproto:         1.0.7-h470a237_2                     conda-forge
    xorg-libice:          1.0.9-h470a237_4                     conda-forge
    xorg-libsm:           1.2.2-h8c8a85c_6                     conda-forge
    xorg-libx11:          1.6.6-h470a237_0                     conda-forge
    xorg-libxau:          1.0.8-h470a237_6                     conda-forge
    xorg-libxdmcp:        1.1.2-h470a237_7                     conda-forge
    xorg-libxext:         1.3.3-h470a237_4                     conda-forge
    xorg-libxrender:      0.9.10-h470a237_2                    conda-forge
    xorg-renderproto:     0.11.1-h470a237_2                    conda-forge
    xorg-xextproto:       7.3.0-h470a237_2                     conda-forge
    xorg-xproto:          7.0.31-h470a237_7                    conda-forge
    xz:                   5.2.4-h470a237_1                     conda-forge
    yaml:                 0.1.7-h470a237_1                     conda-forge
    zlib:                 1.2.11-h470a237_3                    conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... dbus post-link :: /etc/machine-id not found ..
dbus post-link :: .. using /proc/sys/kernel/random/boot_id

done
Solving environment: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/conda-bld/pygtftk_1539260246658/_build_env


The following NEW packages will be INSTALLED:

    binutils_impl_linux-64: 2.31.1-h6176602_1 defaults
    binutils_linux-64:      2.31.1-h6176602_3 defaults
    gcc_impl_linux-64:      7.3.0-habb00fd_1  defaults
    gcc_linux-64:           7.3.0-h553295d_3  defaults
    libgcc-ng:              8.2.0-hdf63c60_1  defaults
    libstdcxx-ng:           8.2.0-hdf63c60_1  defaults

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
INFO: activate-binutils_linux-64.sh made the following environmental changes:
+ADDR2LINE=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-addr2line
+AR=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
+AS=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-as
+CXXFILT=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++filt
+ELFEDIT=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-elfedit
+GPROF=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gprof
+HOST=x86_64-conda_cos6-linux-gnu
+LD_GOLD=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld.gold
+LD=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld
+NM=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-nm
+OBJCOPY=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-objcopy
+OBJDUMP=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-objdump
+RANLIB=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
+READELF=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-readelf
+SIZE=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-size
+STRINGS=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-strings
+STRIP=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
+CC=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
+CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
+CPP=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp
+DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
+GCC_AR=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
+GCC_NM=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
+GCC=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
+GCC_RANLIB=/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
+LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib
CC: /opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/version.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/bedtool_extension.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/cmd_manager.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/settings.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/biomart.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/Line.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/fasta_interface.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/cmd_object.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/tab_interface.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/utils.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/arg_formatter.py -> build/lib.linux-x86_64-3.6/pygtftk
copying pygtftk/gtf_interface.py -> build/lib.linux-x86_64-3.6/pygtftk
creating build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/nb_transcripts.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/convert.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/shift.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_nb_exon.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_numeric_value.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/bed_to_gtf.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/nb_exons.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_intron_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/join_multi_file.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_go.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/add_prefix.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_feat_seq.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/profile.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_loc.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/random_tx.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_5p_3p_coords.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/del_attr.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_most_5p_tx.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/count.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_tx_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/add_exon_nb.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/divergent.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/tss_dist.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/count_key_values.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_attr_value_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/mk_matrix.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_feature_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/intronic.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/tabulate.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_tx_seq.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/intron_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/closest_genes.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/short_long.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/merge_attr.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/col_from_tab.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_max_exon_nb.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/discretize_key.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/feat_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/join_attr.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/apropos.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/seqid_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_example.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/convergent.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/splicing_site.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/get_attr_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/control_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/retrieve.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/random_list.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/midpoints.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_key.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/select_by_regexp.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/overlapping.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/intergenic.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/exon_size.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/convert_ensembl.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/rm_dup_tss.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
copying pygtftk/plugins/coverage.py -> build/lib.linux-x86_64-3.6/pygtftk/plugins
creating build/lib.linux-x86_64-3.6/docs
copying docs/__init__.py -> build/lib.linux-x86_64-3.6/docs
Python version : sys.version_info(major=3, minor=6, micro=6, releaselevel='final', serial=0)
Python path : /opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place
Trying to find an existing .gtftk directory
No .gtftk directory found.
package init file 'docs/source/__init__.py' not found (or not a regular file)
creating build/lib.linux-x86_64-3.6/docs/source
copying docs/source/conf.py -> build/lib.linux-x86_64-3.6/docs/source
creating build/lib.linux-x86_64-3.6/pygtftk/bwig
copying pygtftk/bwig/bw_coverage.py -> build/lib.linux-x86_64-3.6/pygtftk/bwig
copying pygtftk/bwig/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/bwig
creating build/lib.linux-x86_64-3.6/pygtftk/rtools
copying pygtftk/rtools/r_plugin_parser.py -> build/lib.linux-x86_64-3.6/pygtftk/rtools
copying pygtftk/rtools/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/rtools
creating build/lib.linux-x86_64-3.6/pygtftk/data
copying pygtftk/data/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_03
copying pygtftk/data/simple_03/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_03
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_04/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
creating build/lib.linux-x86_64-3.6/pygtftk/data/simple_05
copying pygtftk/data/simple_05/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_05
creating build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
creating build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
copying pygtftk/data/mini_real_noov_rnd_tx/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
creating build/lib.linux-x86_64-3.6/pygtftk/data/control_list
copying pygtftk/data/control_list/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/data/control_list
creating build/lib.linux-x86_64-3.6/pygtftk/src
copying pygtftk/src/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/src
creating build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
creating build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/__init__.py -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying docs/Makefile -> build/lib.linux-x86_64-3.6/docs
copying docs/source/bwig_coverage.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/about.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/api.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/installation.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/developers.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/index.rst -> build/lib.linux-x86_64-3.6/docs/source
copying docs/source/presentation.rst -> build/lib.linux-x86_64-3.6/docs/source
copying pygtftk/data/simple/simple_col.csv -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_mat -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.genes -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_peaks.bed3 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_with_dup -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.2.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.map -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.3.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_peaks.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_peaks.bed6 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.fa.fai -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.bam.bai -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.chromInfo -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_mat_3 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.rev.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.3.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple_reads.fq -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.geneList -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/add_attr_to_pos.tab -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.rev.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.bam -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.loc_bed -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.join_mat_2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.4.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple/simple.fa -> build/lib.linux-x86_64-3.6/pygtftk/data/simple
copying pygtftk/data/simple_02/simple_02.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.join_mat -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.map -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.rev.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02_nbe.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.bam.bai -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.genes -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02_nbe.gtf.old -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.reads.fq -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.rev.2.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.join -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.geneList -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.chromInfo -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02_peaks.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.fa -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.3.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.1.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.4.bt2 -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_02/simple_02.bam -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_02
copying pygtftk/data/simple_03/simple_short_long.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_03
copying pygtftk/data/simple_04/simple.chromInfo -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_04/simple_04.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_04/simple_04.fa -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_04
copying pygtftk/data/simple_05/simple_rm.gtf -> build/lib.linux-x86_64-3.6/pygtftk/data/simple_05
copying pygtftk/data/mini_real/H3K4me3_cond_1.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real_control_1.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/#H3K4me3_cond_1.bed# -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real_counts_ENCFF630HEX.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF431HAA_H3K36me3_K562_sub.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/airway_love.txt.gz -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real.gtf.gz -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF119BYM_H3K36me3_K562_sub.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/tx_classes.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF742FDS_H3K4me3_K562_sub.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/mini_real_gn_list_hg38.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/hg38.genome.back -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF947DVY_H3K79me2_K562_sub.bw -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/hg38.genome -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/H3K4me3_cond_3.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF112BHN_H3K4me3_K562_sub.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/ENCFF354QXX__H3K79me2_K562_sub.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real/H3K4me3_cond_2.bed -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real
copying pygtftk/data/mini_real_noov_rnd_tx/mini_real_noov_rnd_tx.gtf.gz -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
copying pygtftk/data/mini_real_noov_rnd_tx/hg38.genome -> build/lib.linux-x86_64-3.6/pygtftk/data/mini_real_noov_rnd_tx
copying pygtftk/data/control_list/control_list_reference.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/control_list
copying pygtftk/data/control_list/control_list_data.txt -> build/lib.linux-x86_64-3.6/pygtftk/data/control_list
copying pygtftk/src/libgtftk/column.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/README.md -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/gtf_reader.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/globals.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/libgtftk.h -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/version.h -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/libgtftk.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/blast_reader.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk
copying pygtftk/src/libgtftk/command/select_by_genomic_location.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/merge_attr.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/load_blast.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/load_gtf.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/free_raw_data.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/free_gtf_data.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_attributes.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_key.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/get_sequences.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/clear_indexes.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_transcript_size.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/convert_to_ensembl.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_prefix.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_number_of_exon.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_exon_number.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_by_positions.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/del_attributes.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/select_transcript.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/extract_data.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/get_list.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_attr_column.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
copying pygtftk/src/libgtftk/command/add_attr_to_pos.c -> build/lib.linux-x86_64-3.6/pygtftk/src/libgtftk/command
running build_ext
building 'pygtftk/lib/libgtftk' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pygtftk
creating build/temp.linux-x86_64-3.6/pygtftk/src
creating build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk
creating build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/blast_reader.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_attributes.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attributes.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_attr_to_pos.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_to_pos.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/load_blast.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_blast.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/merge_attr.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/merge_attr.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_positions.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_positions.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_attr_column.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_column.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_transcript.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_transcript.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_exon_number.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_exon_number.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/add_prefix.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_prefix.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/libgtftk.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/libgtftk.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/free_raw_data.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_raw_data.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/column.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/column.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/free_gtf_data.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_gtf_data.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_number_of_exon.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_number_of_exon.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/convert_to_ensembl.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/convert_to_ensembl.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/extract_data.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/extract_data.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_genomic_location.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_genomic_location.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/clear_indexes.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/clear_indexes.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/get_list.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_list.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_key.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_key.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/get_sequences.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_sequences.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/globals.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/globals.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/del_attributes.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/del_attributes.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/load_gtf.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_gtf.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/gtf_reader.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/gtf_reader.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
/opt/conda/conda-bld/pygtftk_1539260246658/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -g -fwrapv -O3 -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -Ipygtftk/src/libgtftk -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.6m -c pygtftk/src/libgtftk/command/select_by_transcript_size.c -o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_transcript_size.o -Ipygtftk/src/libgtftk -O3 -Wall -fPIC -MMD -MP -fmessage-length=0 -shared
creating build/lib.linux-x86_64-3.6/pygtftk/lib
gcc -pthread -shared -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -Wl,-rpath=/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib,--no-as-needed -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/blast_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_to_pos.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_blast.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/merge_attr.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_positions.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_attr_column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_transcript.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_exon_number.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/add_prefix.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/libgtftk.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_raw_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/column.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/free_gtf_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_number_of_exon.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/convert_to_ensembl.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/extract_data.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_genomic_location.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/clear_indexes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_list.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_key.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/get_sequences.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/globals.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/del_attributes.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/load_gtf.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/gtf_reader.o build/temp.linux-x86_64-3.6/pygtftk/src/libgtftk/command/select_by_transcript_size.o -L/usr/lib -L/opt/conda/conda-bld/pygtftk_1539260246658/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -lz -lpython3.6m -o build/lib.linux-x86_64-3.6/pygtftk/lib/libgtftk.cpython-36m-x86_64-linux-gnu.so
error: command 'gcc' failed with exit status 1
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: 0.9.7_6ce8e5d235.tar.gz
Downloading https://github.com/dputhier/pygtftk/archive/0.9.7.tar.gz
Success
Extracting download
source tree in: /opt/conda/conda-bld/pygtftk_1539260246658/work
Traceback (most recent call last):
  File "/opt/conda/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 438, in main
    execute(sys.argv[1:])
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 429, in execute
    verify=args.verify)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/api.py", line 201, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 2204, in build_tree
    notest=notest,
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 1445, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir, stats=build_stats)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 313, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 293, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/opt/conda/conda-bld/pygtftk_1539260246658/work/conda_build.sh']' returned non-zero exit status 1.

Segfault when using bed3 files

Using peak_anno with a bed3 file triggers a segfault. No other messages are displayed, even with high verbosity.

Command example :

gtftk peak_anno -i hg38.gtf.gz -c hg38_ensembl.genome -p bed3_h3k4me3.bed -V 3

The command works fine the exact same file is converted to a bed6 with filler characters (eg. 'chr1 100 200' becomes 'chr1 100 200 A B C')

I suspect this is related to the argument formatter and could appear in other parts of the pygtftk project.

peak_anno: idea for new argument "-rpm"

This argument would normalize reads count to RPM (Reads in feature per million reads in sample). This would allow easier comparison of plots produced for different samples. The plot would also contains the normalization factor.

Thx Guillaume.

argparse should not be a dependency

It is part of Python 3. This would install an old version...

Get the closest gene regarding a set of peaks.

closest_gn_to_feat output format

Should be centered on gene or peaks.
Should provided some flexibility about gene features (tts, tss, body).
Is a peak or gene associated with several guys ?

peakanno and default chrom size

The use of a proper set of chromosome size is important for user to get the right stats. I would suggest to provide a set of default chromosome size to users at least for common genomes and version (hs, mm, rn, dm...). This could depend on a function implemented in the utils module that would exploit the pybedtools.helpers.chromsizes(genome) and pybedtools.helpers.chromsizes_to_file(…[, fn]).

Select most common tss among transcript

I was wondering about a command allowing the selection of the most commonly used TSSs among transcripts described for a gene.

gtftk main program complains when an unknow argument is passed

 gtftk -j
 AttributeError: 'ArgumentParser' object has no attribute 'allow_abbrev'

Peak_anno new feature idea: --peak-file taking list instead of only one file

It would imply giving fraction of overlaps instead of number of overlaps which depend on the number of peaks. This would not require so much modifications.

change the argument type to action=a arg_formatter.bedFileList .
Add a novel argument to set order of peak dataset inside bar sets.
Some tuning regarding the R code mainly when writing p-val results.

Thx Guillaume for this idea.

Library is not dynamic

Hello Denis,

I cloned and install this new github repository without problem on blackflag. All is working fine except the library that seems to be not dynamically compiled. Can you check that you compile libgtftk.so with the "-shared" and "-fPIC" options ?

Doc: The gtftk.bam.bam_coverage_matrix module

The title should be related to bwig not bam.

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