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Cat FASTQ files

License: MIT License

Python 100.00%

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smoe tmancill rfetherston aganezov

catfishq's Issues

Add deduplication by read id

-d/--deduplicate

Don't print reads that have been seen before.

Implement q-score computation in C

Current solution is slow

Error when parsing fastq files with empty sequences

Reads with empty sequence field in fastq files are interpreted as fasta entries in output:

@ReadID1
$
+
$
@ReadID2

is outputted like:

ReadID1
$
@ReadID2

Add parameter to specify extensions to look for

Timestamp parsing error

Catfishq returns a timestamp parsing error when using --print-start-time command on FASTQ files generated by Guppy version “5.0.16+b9fcd7b”, likely due to a change in the timestamp format.

Python 3.8, catfishq 1.1.5, pysam 0.17.0

catfishq --print-start-time -r fastq_pass/
Traceback (most recent call last):
  File "/miniconda3/bin/catfishq", line 8, in <module>
    sys.exit(main())
  File "/miniconda3/lib/python3.8/site-packages/catfishq/cat_fastq.py", line 351, in main
    min_start_time=get_start_time(args.FASTQ,args.RECURSIVE)
  File "/miniconda3/lib/python3.8/site-packages/catfishq/cat_fastq.py", line 264, in get_start_time
    min_start_time=compare_start_time(entry.comment,min_start_time)
  File "/miniconda3/lib/python3.8/site-packages/catfishq/cat_fastq.py", line 206, in compare_start_time
    start_time = datetime.strptime(start_time_str,'%Y-%m-%dT%H:%M:%SZ')
  File "/miniconda3/lib/python3.8/_strptime.py", line 568, in _strptime_datetime
    tt, fraction, gmtoff_fraction = _strptime(data_string, format)
  File "/miniconda3/lib/python3.8/_strptime.py", line 349, in _strptime
    raise ValueError("time data %r does not match format %r" %
ValueError: time data '2021-10-19T04:24:16.235874+01:00' does not match format '%Y-%m-%dT%H:%M:%SZ'

LICENSE file not distributed via PyPI

Hello,
The .tar.gz does not offer any license information. Please consider adding the LICENSE file to the archive and to also specify it in setup.py. Ideally, every source file would mention it.
Many thanks!
Steffen (while packaging catfishq for Debian)

TypeError: Argument must be string or unicode

I get the following error on running the following command on catfishq 1.1.15
catfishq -r flowcell_xyz/ --log DEBUG > catf.fastq

Searching flowcell_xyz/ for FASTQ files
Found 622 files
Traceback (most recent call last):
  File "/home/ubuntu/miniconda3/bin/catfishq", line 8, in <module>
    sys.exit(main())
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/catfishq/cat_fastq.py", line 320, in main
    format_fq(
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/catfishq/cat_fastq.py", line 285, in format_fq
    for entry in parse_fastqs(
  File "/home/ubuntu/miniconda3/lib/python3.8/site-packages/catfishq/cat_fastq.py", line 201, in parse_fastqs
    with pysam.FastxFile(filename) as fh:
  File "pysam/cfaidx.pyx", line 456, in pysam.cfaidx.FastxFile.__cinit__
  File "pysam/cfaidx.pyx", line 478, in pysam.cfaidx.FastxFile._open
  File "pysam/cutils.pyx", line 107, in pysam.cutils.encode_filename
TypeError: Argument must be string or unicode.

Thank you.

parser = argparse.ArgumentParser(

Possible alternatives are click or argh (?)

Test pyfastx

Is pyfastx faster than pysam for FASTQ parsing?

Use numpy to compute q-scores more efficiently

catfishq/catfishq/cat_fastq.py

Line 36 in 4c42039

sum_prob += LOOKUP[val]

Check if pysam returns numpy arrays. If it does use numpy to compute probabilities from phred scores more efficiently
Alternative: cython implementation of q-score computation