--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_family_aligner.py	Thu Jun 08 12:46:20 2017 -0400
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+import argparse
+import os
+
+import utils
+
+OUTPUT_DIR = 'geneFamilyAlignments_dir'
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method')
+parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help='Trims alignments using trimAls ML heuristic trimming approach')
+parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help='Flag for constructing orthogroup multiple codon alignments')
+parser.add_argument('--gap_trimming', dest='gap_trimming', default=0, type=float, help='Remove sites in alignments with gaps of')
+parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='Maximum number of iterations')
+parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
+parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets')
+parser.add_argument('--output', dest='output', help='Output dataset')
+parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory')
+parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='Maximum number of iteration that the PASTA algorithm will execute')
+parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
+parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of')
+
+args = parser.parse_args()
+
+# Build the command line.
+cmd = 'GeneFamilyAligner'
+cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
+cmd += ' --alignment_method %s' % args.alignment_method
+if args.alignment_method == 'pasta':
+    if args.pasta_script_path is not None:
+        cmd += ' --pasta_script_path %s' % args.pasta_script_path
+    if args.pasta_iter_limit is not None:
+        cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
+cmd += ' --num_threads %d' % args.num_threads
+if args.codon_alignments is not None:
+    cmd += ' --codon_alignments'
+if args.automated_trimming is not None:
+    cmd += ' --automated_trimming'
+if args.gap_trimming > 0:
+    cmd += ' --gap_trimming %4f' % args.gap_trimming
+if args.remove_sequences > 0:
+    cmd += ' --remove_sequences %4f' % args.remove_sequences
+if args.iterative_realignment > 0:
+    cmd += ' --iterative_realignment %d' % args.iterative_realignment
+
+# Run the command.
+utils.run_command(cmd)
+
+# Handle outputs.
+if args.codon_alignments is None:
+    src_output_dir = OUTPUT_DIR
+else:
+    src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
+utils.move_directory_files(src_output_dir, args.output_dir)
+utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)