Commit 8d8b5b70 authored by Celine Noirot's avatar Celine Noirot
Browse files

Identation error when parsing log.

parent 40550892
......@@ -83,7 +83,6 @@ def mask_sequences (fafile, tab_adapt, len_adapt, options, log, minscore,minmatc
(score, percentMis, primary_match, startFirstMatch, endFirstMatch, secondary_match, startSecondMatch, endSecondMatch)=(int(fm.group(2)), float(fm.group(3)), fm.group(4), int(fm.group(5)), int(fm.group(6)), fm.group(7), int(fm.group(8)), int(fm.group(9)))
save = True
strand = 'fwd'
if line.startswith("Discrepancy summary:"): # This is the end of the section
break
......@@ -92,7 +91,8 @@ def mask_sequences (fafile, tab_adapt, len_adapt, options, log, minscore,minmatc
adaptators_found[primary_match].append([strand, secondary_match, startFirstMatch, endFirstMatch, startSecondMatch, endSecondMatch, score])
except:
adaptators_found[primary_match] = [[strand, secondary_match, startFirstMatch, endFirstMatch, startSecondMatch, endSecondMatch, score]]
log.write("%"+primary_match+"\t"+strand+"\t"+secondary_match+"\t"+str(startFirstMatch)+"\t"+str(endFirstMatch)+"\t"+str(startSecondMatch)+"\t"+str(endSecondMatch)+"\t"+str(score)+"\n")
log.write("%"+primary_match+"\t"+strand+"\t"+secondary_match+"\t"+str(startFirstMatch)+"\t"+str(endFirstMatch)+"\t"+str(startSecondMatch)+"\t"+str(endSecondMatch)+"\t"+str(score)+"\n")
log.write("###Number of sequences with adaptor "+ adapt_ids + " " +str(len(adaptators_found.keys())) +" \n")
......@@ -336,4 +336,4 @@ if __name__ == '__main__':
log.close()
sys.exit(0)
\ No newline at end of file
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