--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multi_glimmer.py	Thu Aug 18 18:50:00 2016 -0400
@@ -0,0 +1,75 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+import argparse
+import os
+import subprocess
+import sys
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Get a multi-fasta, the trained_dir and the output file as inputs, '
+                                                 'to generate GlimmerHMM gene prediction over all contigs')
+
+    parser.add_argument('--multi_fasta', help='Multi fasta file to run GlimmerHMM on', required=True)
+
+    parser.add_argument('--trained_dir', help='Path to the GlimmerHMM trained_dir', required=True)
+
+    parser.add_argument('--output', help='file to output the result into', required=True)
+
+    args = parser.parse_args()
+
+    multi_fasta = args.multi_fasta
+    trained_dir = args.trained_dir
+    # TODO: Temporary fix for the issue with config.file in human/. Next: GC Content to select the appropriate folder
+    if trained_dir.split('/')[-1] == "human":
+        trained_dir = os.path.join(trained_dir, "Train0-43")
+
+    output_file = args.output
+    temp_contig = "temp_contig"
+
+    def exec_glimmer(contig_file, first_time=False):
+        p = subprocess.Popen(["glimmerhmm", contig_file, trained_dir, "-g"],
+                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        output, errors = p.communicate()
+
+        p.wait()
+        # Process the error if != "Done"
+        if not errors or (errors.split()[0] != "Done"):
+            raise Exception("Error in glimmer: {0}".format(errors))
+        else:
+            sys.stdout.write(errors)
+        # If  not first time, we need to remove the first comments
+        if not first_time:
+            output = "\n".join(output.split("\n")[1:])
+
+        return output
+
+    with open(output_file, 'w+') as o:
+        with open(multi_fasta, 'r') as mf:
+            is_first_time = True
+            for i, line in enumerate(mf):
+                if line[0] == '>':
+                    # If it is the first time we finish to read a contig, we let glimmer add the full comments
+                    # and write into the output the result
+                    if is_first_time is True and i != 0:
+                        o.write(exec_glimmer(temp_contig, first_time=is_first_time))
+                        is_first_time = False
+                    # Else we call glimmer and say this is not the first time (so remove the first comment)
+                    # and dump into the output file the result
+                    elif i > 0:
+                        o.write(exec_glimmer(temp_contig))
+
+                    # Because we are on an indication of a beginning of a sequence, we need to create an empty file
+                    # to dump the line into
+                    with open(temp_contig, 'w+') as tc:
+                        tc.write(line)
+                else:
+                    # We are in the sequence of a contig, so we append the line in the file
+                    with open(temp_contig, 'a+') as tc:
+                        tc.write(line)
+        # The file is terminate, we did read another contig so we need to save this last one
+        o.write(exec_glimmer(temp_contig, first_time=is_first_time))
+
+if __name__ == "__main__":
+    main()