diff assembly_post_processor.py @ 77:2849bcb0b7ed draft

Uploaded

--- a/assembly_post_processor.py	Thu Oct 05 14:03:35 2017 -0400
+++ b/assembly_post_processor.py	Thu Oct 05 14:10:50 2017 -0400
@@ -13,14 +13,15 @@
 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('--move_stats', dest='move_stats', default=None, help='Flag to move primary targeted gene families statistics datasets')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of processors')
+parser.add_argument('--output_pttgf', dest='output_pttgf', default=None, help='Primary targeted gene families dataset')
 parser.add_argument('--output_cds', dest='output_cds', help='Output transcripts.cds')
 parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds')
 parser.add_argument('--output_cleaned_nr_cds', dest='output_cleaned_nr_cds', default=None, help='Output transcripts.cleaned.nr.cds')
 parser.add_argument('--output_cleaned_nr_pep', dest='output_cleaned_nr_pep', default=None, help='Output transcripts.cleaned.nr.pep')
 parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep')
 parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep')
+parser.add_argument('--output_pttgf_dir', dest='output_pttgf_dir', default=None, help='Directory hierarchy of targeted gene family datasets')
 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')
@@ -62,10 +63,7 @@
     shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.pep'), args.output_cleaned_nr_pep)
 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.pep'), args.output_cleaned_pep)
 shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.pep'), args.output_pep)
-if args.move_stats is not None:
-    src_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families')
-    dst_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families_statistics')
-    try:
-        shutil.move(os.path.join(src_dir, '*.stats'), dst_dir)
-    except:
-        pass
\ No newline at end of file
+if args.output_pttgf is not None and args.output_pttgf_dir is not None:
+    src_output_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families')
+    utils.move_directory_files(src_output_dir, args.output_pttgf_dir)
+    utils.write_html_output(args.output_pttgf, 'Targeted gene families', args.output_pttgf_dir)
\ No newline at end of file