Mercurial > repos > lgueguen > sartools

comparison pre_sartools.py @ 0:581d217c7337 draft

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Planemo upload
author lgueguen
date Fri, 22 Jul 2016 05:39:13 -0400
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children fe0ee346b17d
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-1:000000000000 0:581d217c7337
1 #!/usr/bin/env python
2 #Author: Coline Billerey
3
4 from os.path import basename, join
5 from os import getcwd, system
6 import argparse
7 from shutil import copyfile
8 import tempfile
9 import csv
10
11 def __main__():
12
13 parser = argparse.ArgumentParser()
14 parser.add_argument('--batch')
15 parser.add_argument('--inputs', action='append' ,nargs='*')
16 parser.add_argument('--outfile')
17 parser.add_argument('--outarch')
18 args = parser.parse_args()
19
20 batch=args.batch
21 outfile=args.outfile
22 outarch=args.outarch
23 inputs=args.inputs
24 counts_files = open( outfile, 'w' )
25
26 working_directory = getcwd()
27 file_zip=working_directory+"/counts.zip"
28
29
30 zip_cmd='zip -j %s' % (file_zip)
31 if batch and batch!="NULL":
32 counts_files.write("label\tfiles\tgroup\tbatch\n")
33 for (level, filename, label, batch_name ) in inputs:
34 filename_base = basename(filename)
35 # For RSEM files we process files as HTSeq count output
36 tmpdir = tempfile.mkdtemp()
37 with open(filename, 'rb') as csvfile:
38 with open(join(tmpdir, basename(filename)), 'wb') as out:
39 spamwriter = csv.writer(out, delimiter='\t')
40 reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
41 if len(reader.fieldnames) > 2:
42 for row in reader:
43 spamwriter.writerow((row['gene_id'], int(float(row['effective_length']))))
44 zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
45 else :
46 zip_cmd += ' %s ' % (filename)
47 counts_files.write( label + "\t" + filename_base + "\t" + level + "\t" + batch_name + "\n" )
48 else :
49 counts_files.write("label\tfiles\tgroup\n")
50 for (level, filename, label) in inputs:
51 filename_base = basename(filename)
52 # For RSEM files we process files as HTSeq count output
53 tmpdir = tempfile.mkdtemp()
54 with open(filename, 'rb') as csvfile:
55 with open(join(tmpdir, basename(filename)), 'wb') as out:
56 spamwriter = csv.writer(out, delimiter='\t')
57 reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
58 if len(reader.fieldnames) > 2:
59 for row in reader:
60 spamwriter.writerow((row['gene_id'], int(float(row['effective_length']))))
61 zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
62 else:
63 zip_cmd += ' %s ' % (filename)
64
65 counts_files.write( label + "\t" + filename_base + "\t" + level + "\n" )
66
67 counts_files.close()
68 system(zip_cmd)
69 copyfile(file_zip,outarch)
70
71
72
73 if __name__=="__main__":
74 __main__()