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changeset 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 d86ccac2a660
files pre_sartools.py
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/pre_sartools.py	Fri Jul 22 05:39:13 2016 -0400
+++ b/pre_sartools.py	Wed Apr 26 05:04:18 2017 -0400
@@ -40,7 +40,7 @@
                     reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
                     if len(reader.fieldnames) > 2:
                         for row in reader:
-                            spamwriter.writerow((row['gene_id'], int(float(row['effective_length']))))
+                            spamwriter.writerow((row['gene_id'], int(float(row['expected_count']))))
                         zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
                     else :
                         zip_cmd += ' %s ' % (filename)
@@ -57,7 +57,7 @@
                     reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
                     if len(reader.fieldnames) > 2:
                         for row in reader:
-                            spamwriter.writerow((row['gene_id'], int(float(row['effective_length']))))
+                            spamwriter.writerow((row['gene_id'], int(float(row['expected_count']))))
                         zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
                     else:
                         zip_cmd += ' %s ' % (filename)