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Reusable tools for working with next-generation sequencing (NGS) data

License: MIT License

Python 99.80% Makefile 0.20%

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sbooeshaghi ziadahmed122 biobenkj yenaled lings01

ngs-tools's Issues

Strandedness of SMART-seq3

Hello ngs-tools team - thank you again for a great tool! I want to ask a question about the strandedness for SMART-seq3. It looks like in the library structure definition within ngs-tools is unstranded. However, looking at zUMIs which was used in the SMART-seq3/SMART-seq3xpress paper, it suggests it's positively stranded. Could you clarify which is correct? Thank you!

Support more technologies

Thanks for the great work! Could you please help add SeqScope and StarMap technology to ngs.chemistry.get_chemistry. And I'm wondering if seqFISH and MERFISH, which are not NGS, can be added too.

Running `get_chemistry('10xFB')` results in error

In the newest version, when running the following one gets the error below.

import ngs_tools
ngs_tools.chemistry.get_chemistry('10xFB')

Error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/test/miniconda3/envs/scrna-seq-wf/lib/python3.8/site-packages/ngs_tools/chemistry/__init__.py", line 91, in get_chemistry
    raise ChemistryError(
ngs_tools.chemistry.Chemistry.ChemistryError: Multiple matching chemistries found: ['10xFBonly', '10xFB']

ngs_tools.gtf.Segment.SegmentError: Invalid segment

Hi,

I am trying to run nf-core/scrnaseq using kallisto aligner. During the step of generating reference index, the following error occurred. It seems to have something to do with segment of zero length. I am using GRCh38.p14 fasta and gtf files from NCBI with appended ERCC transcripts. Do you know how to fix this?

Thank you

Workflow execution completed unsuccessfully


Caused by:
  Missing output file(s) `kb_ref_out.idx` expected by process `NFCORE_SCRNASEQ:SCRNASEQ:KALLISTO_BUSTOOLS:KALLISTOBUSTOOLS_REF (GCF_000001405.40_GRCh38.p14_genomic_ERCC92.fna.gz)`

Command executed:

  kb \
      ref \
      -i kb_ref_out.idx \
      -g t2g.txt \
      -f1 cdna.fa \
      --workflow standard \
      GCF_000001405.40_GRCh38.p14_genomic_ERCC92.fna.gz \
      GCF_000001405.40_GRCh38.p14_genomic_ERCC92.gtf.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCRNASEQ:SCRNASEQ:KALLISTO_BUSTOOLS:KALLISTOBUSTOOLS_REF":
      kallistobustools: $(echo $(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*$//')
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
  [2022-06-28 15:54:36,355] WARNING [main] Gene `RNU6-222P_21` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_21`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR2DP1_29` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_29`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR3DP1_32` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_32`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `RNU6-222P_22` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_22`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR3DP1_33` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_33`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR2DP1_30` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_30`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR2DP1_31` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_31`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR3DP1_34` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_34`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `RNU6-222P_23` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_23`.
  [2022-06-28 15:54:36,355] WARNING [main] Gene `KIR2DP1_32` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_32`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `KIR3DP1_35` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_35`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `RNU6-222P_24` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_24`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `KIR2DP1_33` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_33`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `KIR3DP1_36` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_36`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `RNU6-222P_25` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_25`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `KIR3DP1_37` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_37`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `RNU6-222P_26` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_26`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `KIR2DP1_34` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_34`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `KIR3DP1_38` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_38`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `RNU6-222P_27` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_27`.
  [2022-06-28 15:54:36,356] WARNING [main] Gene `RNU6-222P_28` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_28`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `KIR3DP1_39` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_39`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `KIR2DP1_35` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_35`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `RNU6-222P_29` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_29`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `KIR3DP1_40` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_40`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `KIR2DP1_36` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_36`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `RNU6-222P_30` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_30`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `KIR3DP1_41` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_41`.
  [2022-06-28 15:54:36,357] WARNING [main] Gene `KIR2DP1_37` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_37`.
  [2022-06-28 15:54:36,358] WARNING [main] Gene `RNU6-222P_31` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `RNU6-222P_31`.
  [2022-06-28 15:54:36,358] WARNING [main] Gene `KIR3DP1_42` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_42`.
  [2022-06-28 15:54:36,358] WARNING [main] Gene `KIR2DP1_38` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR2DP1_38`.
  [2022-06-28 15:54:36,358] WARNING [main] Gene `KIR3DP1_43` has no transcripts. The entire gene will be marked as a transcript and an exon with ID `KIR3DP1_43`.
  [2022-06-28 15:54:41,332]   ERROR [main] An exception occurred
  Traceback (most recent call last):
    File "/usr/local/lib/python3.9/site-packages/kb_python/main.py", line 856, in main
      COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir)
    File "/usr/local/lib/python3.9/site-packages/kb_python/main.py", line 168, in parse_ref
      ref(
    File "/usr/local/lib/python3.9/site-packages/ngs_tools/logging.py", line 62, in inner
      return func(*args, **kwargs)
    File "/usr/local/lib/python3.9/site-packages/kb_python/ref.py", line 393, in ref
      gene_infos, transcript_infos = ngs.gtf.genes_and_transcripts_from_gtf(
    File "/usr/local/lib/python3.9/site-packages/ngs_tools/gtf/__init__.py", line 190, in genes_and_transcripts_from_gtf
      introns = exons.invert(transcript_interval)
    File "/usr/local/lib/python3.9/site-packages/ngs_tools/gtf/SegmentCollection.py", line 108, in invert
      Segment(self._segments[i].end, self._segments[i + 1].start)
    File "/usr/local/lib/python3.9/site-packages/ngs_tools/gtf/Segment.py", line 27, in __init__
      raise SegmentError(f'Invalid segment [{start}:{end})')
  ngs_tools.gtf.Segment.SegmentError: Invalid segment [1095094:1095094)

Work dir:
  s3://***

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`````

Dependency pysam issue installing on Windows

pysam appears to be incompatible with Windows. Is there a workaround that has worked with Windows users in the past? (exact error message below in case it's helpful)

On `pip install ngs-tools':

Requirement already satisfied: ngs-tools in c:\users\danie.conda\envs\islands_spateo\lib\site-packages\ngs_tools-1.8.0-py3.9.egg (1.8.0)
Collecting joblib>=1.0.1
Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB)
Requirement already satisfied: numba>=0.53.1 in c:\users\danie.conda\envs\islands_spateo\lib\site-packages\numba-0.56.0-py3.9-win-amd64.egg (from ngs-tools) (0.56.0)
Requirement already satisfied: numpy>=1.19.0 in c:\users\danie.conda\envs\islands_spateo\lib\site-packages (from ngs-tools) (1.23.2)
Collecting pysam>=0.16.0.1
Using cached pysam-0.19.1.tar.gz (3.9 MB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [24 lines of output]
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
'.' is not recognized as an internal or external command,
operable program or batch file.
'.' is not recognized as an internal or external command,
operable program or batch file.
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "C:\Users\danie\AppData\Local\Temp\pip-install-r3sizz6x\pysam_e7b73877fc3c476cbb4001e186c76802\setup.py", line 375, in
htslib_make_options = run_make_print_config()
File "C:\Users\danie\AppData\Local\Temp\pip-install-r3sizz6x\pysam_e7b73877fc3c476cbb4001e186c76802\setup.py", line 74, in run_make_print_config
stdout = subprocess.check_output(["make", "-s", "print-config"])
File "C:\Users\danie.conda\envs\islands_spateo\lib\subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "C:\Users\danie.conda\envs\islands_spateo\lib\subprocess.py", line 505, in run
with Popen(*popenargs, **kwargs) as process:
File "C:\Users\danie.conda\envs\islands_spateo\lib\subprocess.py", line 951, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Users\danie.conda\envs\islands_spateo\lib\subprocess.py", line 1420, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified
# pysam: htslib configure options: None
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

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