--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pre_sartools.py	Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+#Author: Coline Billerey
+
+from os.path import  basename, join
+from os import getcwd, system
+import argparse
+from shutil import copyfile
+import tempfile
+import csv
+
+def __main__():
+    
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--batch')
+    parser.add_argument('--inputs', action='append' ,nargs='*')
+    parser.add_argument('--outfile')
+    parser.add_argument('--outarch')
+    args = parser.parse_args()
+
+    batch=args.batch
+    outfile=args.outfile
+    outarch=args.outarch
+    inputs=args.inputs
+    counts_files = open( outfile, 'w' )
+
+    working_directory = getcwd()
+    file_zip=working_directory+"/counts.zip"
+
+
+    zip_cmd='zip -j %s' % (file_zip)
+    if batch and batch!="NULL":
+        counts_files.write("label\tfiles\tgroup\tbatch\n")
+        for (level, filename, label, batch_name ) in inputs:
+            filename_base = basename(filename)
+            # For RSEM files we process files as HTSeq count output
+            tmpdir = tempfile.mkdtemp()
+            with open(filename, 'rb') as csvfile:
+                with open(join(tmpdir, basename(filename)), 'wb') as out:
+                    spamwriter = csv.writer(out, delimiter='\t')
+                    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']))))
+                        zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
+                    else :
+                        zip_cmd += ' %s ' % (filename)
+            counts_files.write( label + "\t" + filename_base + "\t" + level + "\t" + batch_name + "\n" )
+    else :
+        counts_files.write("label\tfiles\tgroup\n")
+        for (level, filename, label) in inputs:
+            filename_base = basename(filename)
+            # For RSEM files we process files as HTSeq count output
+            tmpdir = tempfile.mkdtemp()
+            with open(filename, 'rb') as csvfile:
+                with open(join(tmpdir, basename(filename)), 'wb') as out:
+                    spamwriter = csv.writer(out, delimiter='\t')
+                    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']))))
+                        zip_cmd += ' %s ' % (join(tmpdir, basename(filename)))
+                    else:
+                        zip_cmd += ' %s ' % (filename)
+
+            counts_files.write( label + "\t" + filename_base + "\t" + level + "\n" )
+
+    counts_files.close()
+    system(zip_cmd)
+    copyfile(file_zip,outarch)
+
+
+
+if __name__=="__main__": 
+    __main__()