Mercurial > repos > peterjc > seq_primer_clip
diff tools/seq_primer_clip/seq_primer_clip.py @ 5:530c8d6fedd8 draft
v0.0.15 - internal changes
author | peterjc |
---|---|
date | Wed, 10 May 2017 13:09:52 -0400 |
parents | 9b074c1db68e |
children | b9dc7c967ee6 |
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--- a/tools/seq_primer_clip/seq_primer_clip.py Thu Feb 02 11:52:37 2017 -0500 +++ b/tools/seq_primer_clip/seq_primer_clip.py Wed May 10 13:09:52 2017 -0400 @@ -29,8 +29,10 @@ NOTE: Currently it uses Python's regular expression engine for finding the primers, which for my needs is fast enough. """ + +import re import sys -import re + from galaxy_utils.sequence.fasta import fastaReader, fastaWriter from galaxy_utils.sequence.fastq import fastqReader, fastqWriter @@ -147,8 +149,8 @@ # We'll use a set to remove any duplicate patterns # if letter not in "NX": pattern = seq[:i] + "N" + seq[i + 1:] - assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \ - % (pattern, len(pattern), seq, len(seq)) + assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i" + % (pattern, len(pattern), seq, len(seq))) yield make_reg_ex(pattern) if mm >= 2: for i, letter in enumerate(seq): @@ -158,8 +160,8 @@ # We'll use a set to remove any duplicate patterns # if letter not in "NX": pattern = seq[:i] + "N" + seq[i + 1:i + 1 + k] + "N" + seq[i + k + 2:] - assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \ - % (pattern, len(pattern), seq, len(seq)) + assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i" + % (pattern, len(pattern), seq, len(seq))) yield make_reg_ex(pattern)