Mercurial > repos > lgueguen > sartools

comparison pre_sartools.py @ 1:fe0ee346b17d draft

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RSEM process files corrected in pre_sartools.py
author lgueguen
date Wed, 26 Apr 2017 05:04:18 -0400
parents 581d217c7337
children 05c9b1a7f44e
comparison
equal deleted inserted replaced
0:581d217c7337 1:fe0ee346b17d
38 with open(join(tmpdir, basename(filename)), 'wb') as out: 38 with open(join(tmpdir, basename(filename)), 'wb') as out:
39 spamwriter = csv.writer(out, delimiter='\t') 39 spamwriter = csv.writer(out, delimiter='\t')
40 reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True) 40 reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
41 if len(reader.fieldnames) > 2: 41 if len(reader.fieldnames) > 2:
42 for row in reader: 42 for row in reader:
43 spamwriter.writerow((row['gene_id'], int(float(row['effective_length'])))) 43 spamwriter.writerow((row['gene_id'], int(float(row['expected_count']))))
44 zip_cmd += ' %s ' % (join(tmpdir, basename(filename))) 44 zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
45 else : 45 else :
46 zip_cmd += ' %s ' % (filename) 46 zip_cmd += ' %s ' % (filename)
47 counts_files.write( label + "\t" + filename_base + "\t" + level + "\t" + batch_name + "\n" ) 47 counts_files.write( label + "\t" + filename_base + "\t" + level + "\t" + batch_name + "\n" )
48 else : 48 else :
55 with open(join(tmpdir, basename(filename)), 'wb') as out: 55 with open(join(tmpdir, basename(filename)), 'wb') as out:
56 spamwriter = csv.writer(out, delimiter='\t') 56 spamwriter = csv.writer(out, delimiter='\t')
57 reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True) 57 reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
58 if len(reader.fieldnames) > 2: 58 if len(reader.fieldnames) > 2:
59 for row in reader: 59 for row in reader:
60 spamwriter.writerow((row['gene_id'], int(float(row['effective_length'])))) 60 spamwriter.writerow((row['gene_id'], int(float(row['expected_count']))))
61 zip_cmd += ' %s ' % (join(tmpdir, basename(filename))) 61 zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
62 else: 62 else:
63 zip_cmd += ' %s ' % (filename) 63 zip_cmd += ' %s ' % (filename)
64 64
65 counts_files.write( label + "\t" + filename_base + "\t" + level + "\n" ) 65 counts_files.write( label + "\t" + filename_base + "\t" + level + "\n" )