changeset 46:b7858b1f64f1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/assembly_post_processor.py	Wed May 03 10:14:03 2017 -0400
@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+import argparse
+import os
+import subprocess
+
+import utils
+
+OUTPUT_DIR = 'assemblyPostProcessor_dir'
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences')
+parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments')
+parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families')
+parser.add_argument('--method', dest='method', default=None, help='Protein clustering method')
+parser.add_argument('--min_length', dest='min_length', type=int, default=0, help='Minimum sequence length')
+parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of processors')
+parser.add_argument('--prediction_method', dest='prediction_method', help='Coding regions prediction method')
+parser.add_argument('--scaffold', dest='scaffold', default=None, help='Gene family scaffold')
+parser.add_argument('--score_matrices', dest='score_matrices', default=None, help='Scores matrices')
+parser.add_argument('--strand_specific', dest='strand_specific', default=None, help='Strand-specific assembly')
+parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file')
+
+args = parser.parse_args()
+
+# Build the command line.
+cmd = 'AssemblyPostProcessor'
+if args.dereplicate is not None:
+    cmd += ' --dereplicate'
+if args.gap_trimming > 0:
+    cmd += ' --gap_trimming %4f' % args.gap_trimming
+if args.gene_family_search is not None:
+    cmd += ' --gene_family_search %s' % args.gene_family_search
+if args.method is not None:
+    cmd += ' --method %s' % args.method
+if args.min_length > 0:
+    cmd += ' --min_length %d' % args.min_length
+cmd += ' --num_threads %d' % args.num_threads
+cmd += ' --prediction_method %s' % args.prediction_method
+if args.scaffold is not None:
+    cmd += ' --scaffold %s' % args.scaffold
+if args.score_matrices is not None:
+    cmd += ' --score_matrices %s' % args.score_matrices
+if args.strand_specific is not None:
+    cmd += ' --strand_specific'
+cmd += ' --transcripts %s' % args.transcripts
+
+# Run the command.
+proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
+rc = proc.wait()
+utils.check_execution_errors(rc, proc.stderr, proc.stdout)