Mercurial > repos > davidvanzessen > imgt_convert
changeset 1:83cb18fb0a87 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 13 Nov 2013 09:46:37 -0500 |
| parents | 14e80e5c3353 |
| children | b5a2cd3210fa |
| files | imgtconvert.py |
| diffstat | 1 files changed, 11 insertions(+), 7 deletions(-) [+] |
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--- a/imgtconvert.py Wed Nov 13 09:36:48 2013 -0500 +++ b/imgtconvert.py Wed Nov 13 09:46:37 2013 -0500 @@ -3,6 +3,9 @@ import argparse import os +def stop_err( msg, ret=1 ): + sys.stderr.write( msg ) + sys.exit( ret ) #docs.python.org/dev/library/argparse.html parser = argparse.ArgumentParser() @@ -19,17 +22,18 @@ added_sequence_columns = [u'FR1-IMGT', u'FR2-IMGT', u'FR3-IMGT', u'CDR3-IMGT', u'JUNCTION', u'J-REGION', u'FR4-IMGT'] added_junction_columns = [u"P3'V-nt nb", u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb"] +inputFolder = args.input -dirContents = os.listdir(args.input) +dirContents = os.listdir(inputFolder) if len(dirContents) == 1: - if os.path.isdir(dirContents[0]): - dirContents = os.listdir(dirContents[0]) -files = sorted([os.path.join(args.input, f) for f in dirContents]) - -print files + inputFolder = os.path.join(inputFolder, dirContents[0]) + if os.path.isdir(inputFolder): + print "is dir" + dirContents = os.listdir(inputFolder) +files = sorted([os.path.join(inputFolder, f) for f in dirContents]) if len(files) % 3 is not 0: - print "Files in zip not a multiple of 3, it should contain the all the 1_, 5_ and 6_ files for a sample" + stop_err("Files in zip not a multiple of 3, it should contain the all the 1_, 5_ and 6_ files for a sample") import sys sys.exit()