# HG changeset patch
# User lgueguen
# Date 1493197458 14400
# Node ID fe0ee346b17dbe0c2403d51067c3da7c00c86cc4
# Parent  581d217c7337009b078c793fc5b52acb87b5b0e9
RSEM process files corrected in pre_sartools.py

diff -r 581d217c7337 -r fe0ee346b17d pre_sartools.py
--- 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)