--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_family_classifier.py	Thu Jun 08 12:48:23 2017 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+import argparse
+import os
+import shutil
+
+import utils
+
+
+BUFF_SIZE = 1048576
+OUTPUT_DIR = 'geneFamilyClassification_dir'
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--input', dest='input', help='Input dataset')
+parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
+parser.add_argument('--method', dest='method', help='Protein clustering method')
+parser.add_argument('--classifier', dest='classifier', help='Protein classification method')
+parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
+parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
+parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification')
+parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration')
+parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=0, help='Minimum single copy taxa required in orthogroup')
+parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup')
+parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
+parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
+parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
+parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file')
+parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups')
+parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
+parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences')
+parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
+parser.add_argument('--output_ptsco', dest='output_ptsco', default=None, help='Output for single copy orthogroups')
+parser.add_argument('--output_ptsco_dir', dest='output_ptsco_dir', default=None, help='output_ptsco.files_path')
+
+args = parser.parse_args()
+
+# Build the command line.
+cmd = 'GeneFamilyClassifier'
+cmd += ' --proteins %s' % args.input
+cmd += ' --scaffold %s' % args.scaffold
+cmd += ' --method %s' % args.method
+cmd += ' --classifier %s' % args.classifier
+cmd += ' --config_dir %s' % args.config_dir
+cmd += ' --num_threads %d' % args.num_threads
+if args.super_orthogroups is not None:
+    cmd += ' --super_orthogroups %s' % args.super_orthogroups
+if args.single_copy_custom is not None:
+    cmd += ' --single_copy_custom %s' % args.single_copy_custom
+if args.single_copy_taxa > 0:
+    cmd += ' --single_copy_taxa %d' % args.single_copy_taxa
+if args.taxa_present > 0:
+    cmd += ' --taxa_present %d' % args.taxa_present
+if args.orthogroup_fasta is None:
+    create_ortho_sequences = False
+else:
+    create_ortho_sequences = True
+    cmd += ' --orthogroup_fasta'
+if args.coding_sequences is None:
+    create_corresponding_coding_sequences = False
+else:
+    create_corresponding_coding_sequences = True
+    cmd += ' --coding_sequences %s' % args.coding_sequences
+
+# Run the command.
+utils.run_command(cmd)
+
+# Handle hmmscan.log output.
+if args.classifier in ['hmmscan', 'both']:
+    src_hmmscan_log = os.path.join(OUTPUT_DIR, 'hmmscan.log')
+    if os.path.exists(src_hmmscan_log):
+        if args.save_hmmscan_log is None:
+            os.remove(src_hmmscan_log)
+        else:
+            shutil.move(src_hmmscan_log, args.hmmscan_log)
+
+# Handle orthogroups outputs.
+if create_ortho_sequences:
+    if create_corresponding_coding_sequences:
+        out_file = args.output_ptorthocs
+        orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
+        title = 'Orthogroups and corresponding coding sequences files'
+    else:
+        out_file = args.output_ptortho
+        orthogroups_fasta_dest_dir = args.output_ptortho_dir
+        title = 'Orthogroups files'
+    orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
+    utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir)
+    utils.write_html_output(out_file, title, orthogroups_fasta_dest_dir)
+
+# Handle single copy orthogroup outputs.
+if args.output_ptsco is not None:
+    single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
+    single_copy_fasta_dest_dir = args.output_ptsco_dir
+    title = 'Single copy orthogroups files'
+    utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
+    utils.write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)