Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 38:7b2c40450792 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty
| author | pjbriggs |
|---|---|
| date | Wed, 17 Oct 2018 05:01:57 -0400 |
| parents | e832be1635b4 |
| children | d19fca1c009c |
| files | amplicon_analysis_pipeline.py |
| diffstat | 1 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.py Tue Oct 16 10:54:44 2018 -0400 +++ b/amplicon_analysis_pipeline.py Wed Oct 17 05:01:57 2018 -0400 @@ -60,9 +60,10 @@ sys.stderr.write("%s\n\n" % ('*'*width)) def clean_up_name(sample): - # Remove trailing "_L[0-9]+_001" from Fastq - # pair names - split_name = sample.split('_') + # Remove extensions and trailing "_L[0-9]+_001" from + # Fastq pair names + sample_name = '.'.join(sample.split('.')[:1]) + split_name = sample_name.split('_') if split_name[-1] == "001": split_name = split_name[:-1] if split_name[-1].startswith('L'): @@ -152,6 +153,7 @@ fastqs = iter(args.fastq_pairs) for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs): sample_name = clean_up_name(sample_name) + print "Cleaned up sample name: %s" % sample_name r1 = "%s_R1_.fastq" % sample_name r2 = "%s_R2_.fastq" % sample_name os.symlink(fqr1,r1)