Mercurial > repos > greg > plant_tribes_assembly_post_processor
view assembly_post_processor.py @ 0:fcc558568020 draft
Uploaded
author | greg |
---|---|
date | Thu, 08 Jun 2017 12:44:09 -0400 |
parents | |
children |
line wrap: on
line source
#!/usr/bin/env python import argparse import os import shutil import utils OUTPUT_DIR = 'assemblyPostProcessing_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('--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') 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. utils.run_command(cmd) # Handle outputs. shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cds'), args.output_cds) shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.cds'), args.output_cleaned_cds) if args.output_cleaned_nr_cds is not None: shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.cds'), args.output_cleaned_nr_cds) if args.output_cleaned_nr_pep is not None: 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.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)