changeset 77:98c2a9f97e83 draft

Uploaded

--- a/phylogenomics_analysis.py	Wed Mar 22 11:29:27 2017 -0400
+++ b/phylogenomics_analysis.py	Wed Mar 22 11:29:46 2017 -0400
@@ -11,32 +11,33 @@
 
 parser = argparse.ArgumentParser()
 
-parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Input dataset files_path")
-parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
+parser.add_argument('--alignments_method', dest='alignments_method', default=None, help='Multiple sequence alignments method')
+parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
+parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments")
+parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
+parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of')
+parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, default=None, help='Maximum number of sequences in orthogroup alignments')
 parser.add_argument('--method', dest='method', help='Protein clustering method')
-parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
+parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, default=None, help='Minimum number of sequences in orthogroup alignments')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
+parser.add_argument('--output_aln', dest='output_aln', default=None, help='Output for orthogroups alignments')
+parser.add_argument('--output_aln_dir', dest='output_aln_dir', default=None, help='output_aln.files_path')
+parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Input dataset files_path")
 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help="Flag for coding sequences associated with orthogroups")
-parser.add_argument('--sequence_type', dest='sequence_type', default=None, help="Sequence type used in the phylogenetic inference")
-parser.add_argument('--alignments_method', dest='alignments_method', default=None, help='Multiple sequence alignments method')
-parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
-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('--tree_inference', dest='tree_inference', default=None, help='Phylogenetic trees inference method')
-parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
-parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
-parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, default=None, help='Maximum number of sequences in orthogroup alignments')
-parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, default=None, help='Minimum number of sequences in orthogroup alignments')
-parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of')
-parser.add_argument('--trim_type', dest='trim_type', default=None, help='Process used for gap trimming')
-parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of')
 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_aln', dest='output_aln', default=None, help='Output for orthogroups alignments')
-parser.add_argument('--output_aln_dir', dest='output_aln_dir', default=None, help='output_aln.files_path')
+parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
 parser.add_argument('--output_tree', dest='output_tree', default=None, help='Output for phylogenetic trees')
 parser.add_argument('--output_tree_dir', dest='output_tree_dir', default=None, help='output_tree.files_path')
+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=None, type=float, help='Remove sequences with gaps of')
+parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
+parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
+parser.add_argument('--sequence_type', dest='sequence_type', default=None, help="Sequence type used in the phylogenetic inference")
+parser.add_argument('--tree_inference', dest='tree_inference', default=None, help='Phylogenetic trees inference method')
+parser.add_argument('--trim_type', dest='trim_type', default=None, help='Process used for gap trimming')
 
 args = parser.parse_args()
 
@@ -119,6 +120,8 @@
 cmd += ' --config_dir %s' % args.config_dir
 cmd += ' --num_threads %d' % args.num_threads
 
+if args.codon_alignments is not None:
+    cmd += ' --codon_alignments'
 if args.orthogroup_fna is not None:
     cmd += ' --orthogroup_fna'
 if args.sequence_type is not None: