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argparse bug when running consolidate #78
Description
After succesfully running demultiplex and unitag, I tried running consolidate step with the following command:
SAMPLE=test
guideseq.py consolidate \
--read1 $WORKDIR/umitagged/${SAMPLE}.r1.umitagged.fastq \
--read2 $WORKDIR/umitagged/${SAMPLE}.r2.umitagged.fastq \
--outfolder $WORKDIR I got the following error
[09/27 07:33:18PM][INFO][guideseq_cmd] Consolidating reads...
[09/27 07:33:18PM][ERROR][guideseq_cmd] Error umitagging
[09/27 07:33:18PM][ERROR][guideseq_cmd] Traceback (most recent call last):
File "/users/rng/mambaforge/envs/guideseq/lib/python3.7/site-packages/guideseq/guideseq_cmd.py", line 186, in consolidate
consolidate.consolidate(self.umitagged[sample]['read1'], self.consolidated[sample]['read1'], min_qual, min_freq)
File "/users/rng/mambaforge/envs/guideseq/lib/python3.7/site-packages/umi/consolidate.py", line 92, in consolidate
consolidation_sucess, cons_seq, cons_qual = zip(*[consolidate_position(bases, quals, min_qual, min_freq) for bases, quals in zip(read_bases, read_quals)])
File "/users/rng/mambaforge/envs/guideseq/lib/python3.7/site-packages/umi/consolidate.py", line 92, in <listcomp>
consolidation_sucess, cons_seq, cons_qual = zip(*[consolidate_position(bases, quals, min_qual, min_freq) for bases, quals in zip(read_bases, read_quals)])
File "/users/rng/mambaforge/envs/guideseq/lib/python3.7/site-packages/umi/consolidate.py", line 49, in consolidate_position
if qq > min_qual:
TypeError: '>' not supported between instances of 'int' and 'NoneType'
I then investigated this by calling consolidate from umi.consolidate directly in a python environment and didn't run into an error.
I then looked into the guideseq.py script that handles command line arguments. I modified the script to print out the values of min_qual and min_freq before it runs g.consolidate(...). Turns out both values are None.
In the following lines, the conditional is evaluated as True, even when these optional arguments are not provided.
if 'min_quality' in args:
min_qual = args.min_quality
else:
min_qual = CONSOLIDATE_MIN_QUAL
if 'min_frequency' in args:
min_freq = args.min_frequency
else:
min_freq = CONSOLIDATE_MIN_FREQThe program works after I have changed these lines to the following:
if args.min_quality is not None:
min_qual = args.min_quality
else:
min_qual = CONSOLIDATE_MIN_QUAL
if args.min_frequency is not None:
min_freq = args.min_frequency
else:
min_freq = CONSOLIDATE_MIN_FREQ
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