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fixchr's Issues

bioconda package

Hi,

It says in the readme that a bioconda package is a TODO item. Are you happy to create one? Or I can do it if you like. My only hesitation is that if you want to create a pypi release this will change the bioconda recipe compared to if you don't want to create a pypi package (in which case you would just need to rely on github releases)

UnboundLocalError

Hello again.

Although I've had success using fixchr on some scaffolds, I'm still struggling with the original ones that needed reversecomplementing despite generating pafs and sams with different flags in minimap2. Here's the paf generation with error:

$minimap2 -cx asm20 -L --eqx BAR3230_D13.fasta PSC355_D13.fasta >> PSC355xBAR3230_D13.paf

fixchr:

$fixchr -c PSC355xBAR3230_D13.paf -r BAR3230_D13.fasta -q PSC355_D13.fasta -F P --prefix D13_PSC355xBAR3230

#error 
Traceback (most recent call last):
  File "/home/test/miniconda3/bin/fixchr", line 4, in <module>
    __import__('pkg_resources').run_script('fixchr==0.1', 'fixchr')
  File "/home/test/miniconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 662, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/test/miniconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1466, in run_script
    exec(script_code, namespace, namespace)
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.1-py3.8.egg/EGG-INFO/scripts/fixchr", line 6, in <module>
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.1-py3.8.egg/fixchr/scripts/fixchr.py", line 105, in main
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.1-py3.8.egg/fixchr/scripts/fixchr.py", line 63, in fixchr
  File "/home/test/miniconda3/lib/python3.8/site-packages/fixchr-0.1-py3.8.egg/fixchr/scripts/func.py", line 632, in homchr
UnboundLocalError: local variable 'coords2' referenced before assignment

thanks!

How to keep original order of contigs?

Hi,

Thank you for making this tool. I've corrected the contig orientation and generated plots using FicChr; however my contigs are out of order.
This is a species1areference vs species1bquery
All chromosomes are arranged from ch1-ch24 in the original .fasta files, both before and after orientation fixing. Is there a way to correct this?
In the instructions it mentions an .agp file-- I do not have this for my assemblies (is there a tool out there which generates this?), or is there an easier way to correct this?

image

ERROR astart is not int

Hello I'm looking to determine variants between to homologous chromosomes by mapping a whole genome sequence to a reference chromosome via minimap2 and fixchr:

$ minimap2 -x asm20 --eqx Chrom24_CM040141_Aggsing.fa Agt_singleline.mfa >> Chr24_Chr10GST_AggxAgt_20.paf

fixchr -c Chr24_Chr10GST_AggxAgt_20.paf -r Chrom24_CM040141_Aggsing.fa -q Agt_singleline.mfa

but I keep getting an error with the paf, do the files need to be compressed?

Reading Coords - ERROR - astart is not int

Thank you

Installation error

When I install the software running "python setup.py install", the error occurs:
Traceback`(most recent call last):

File "/data/01/user157/software/fixchr/setup.py", line 18, in <module>
  long_description=open('README.rst').read(),
FileNotFoundError: [Errno 2] No such file or directory: 'README.rst'

I can not find the file "README.rst". Could you give me any suggestions?

--prefix not used

Dear developers

I ran:

/path/to/apps/fixchr/bin/fixchr \
-c /path/to/some_comparative_genomics/syri_Hp1_to_pm1.delta.m.coords \
-r /path/to/some_comparative_genomics/assembly_pm1_v1_upper.fasta \
-q /path/to/some_comparative_genomics/Hp1.fasta \
--contig_size 5000 \
--dir /path/to/some_comparative_genomics/ \
--prefix Hp1_to_pm1

but the output had no prefix whatsoever.

ref.filtered.fa
qry.filtered.fa
homologous_strand_corrected.pdf
homologous_strand_corrected_alignments.txt
homologous_alignments.txt
homologous.pdf
input.pdf
input_alignments.txt

Which is harmless, unless you run more than one instance.

Kind regards,

AWebb

Reading BAM/SAM file - ERROR - CIGAR string is not present in PAF at line 2364 8479 37257382 37251209 6116 6174 95.73 1 -1 chr01 chr22. Exiting

Hi Manish，
when I run 'fixchr -c S.P.filter.coords -r S.genome.fa -q P.genome.fa -F P',it showed 'Reading BAM/SAM file - ERROR - CIGAR string is not present in PAF at line 2364 8479 37257382 37251209 6116 6174 95.73 1 -1 chr01 chr22. Exiting.' .The S.P.filter.coords file is the output of 'show-coords -THrd' .
I'm wondering which file should be the input(alignment.paf) for fixchr and how to get it ?
Best,
Lily

hometools..? 

          Thanks for the update! I believe I've reinstalled all of the dependencies and pulled the newest version 0.2, but now I'm running into a "hometools" no module issue. I've tried to install this using the standard conda install and python pip to no avail. I see this in the func.py script, line 45 but nowhere else...?

Originally posted by @cistarsa in #3 (comment)

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