--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer_wo_icm.py	Tue Nov 28 10:08:06 2017 -0500
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+"""
+Input: DNA Fasta File
+Output: Tabular
+Return Tabular File with predicted ORF's
+Bjoern Gruening
+"""
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+from glimmer2seq import glimmer2seq
+
+
+def main():
+    genome_seq_file = sys.argv[1]
+    outfile_classic_glimmer = sys.argv[2]
+    outfile_ext_path = sys.argv[3]
+    oufile_genes = sys.argv[8]
+
+    tag = 'glimmer_non_knowlegde_based_prediction'
+    tempdir = tempfile.gettempdir()
+
+    trainingset = os.path.join(tempdir, tag + ".train")
+    icm = os.path.join(tempdir, tag + ".icm")
+
+    longorfs = tempfile.NamedTemporaryFile()
+    trainingset = tempfile.NamedTemporaryFile()
+    icm = tempfile.NamedTemporaryFile()
+
+    # glimmeropts = "-o0 -g110 -t30 -l"
+    glimmeropts = "-o%s -g%s -t%s" % (sys.argv[4], sys.argv[5], sys.argv[6])
+    if sys.argv[7] == "true":
+        glimmeropts += " -l"
+
+    """
+        1. Find long, non-overlapping orfs to use as a training set
+    """
+    subprocess.Popen(["long-orfs", "-n", "-t", "1.15",
+                      genome_seq_file, "-"], stdout=longorfs,
+                     stderr=subprocess.PIPE).communicate()
+
+    """
+        2. Extract the training sequences from the genome file
+    """
+    subprocess.Popen(["extract", "-t",
+                      genome_seq_file, longorfs.name], stdout=trainingset,
+                     stderr=subprocess.PIPE).communicate()
+
+    """
+        3. Build the icm from the training sequences
+    """
+
+    # the "-" parameter is used to redirect the output to stdout
+    subprocess.Popen(["build-icm", "-r", "-"],
+                     stdin=open(trainingset.name), stdout=icm,
+                     stderr=subprocess.PIPE).communicate()
+
+    """
+        Run Glimmer3
+    """
+    subprocess.Popen(["glimmer3", glimmeropts,
+                      genome_seq_file, icm.name, os.path.join(tempdir, tag)],
+                     stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+
+    if outfile_classic_glimmer.strip() != 'None':
+        shutil.copyfile(os.path.join(tempdir, tag + ".predict"), outfile_classic_glimmer)
+    if outfile_ext_path.strip() != 'None':
+        shutil.copyfile(os.path.join(tempdir, tag + ".detail"), outfile_ext_path)
+
+    glimmer2seq(os.path.join(tempdir, tag + ".predict"), genome_seq_file, oufile_genes)
+
+
+if __name__ == "__main__":
+    main()