comparison assembly_post_processor.py @ 54:9a105e8f08e5 draft

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53:0f65703d5bb8

#!/usr/bin/env python
import argparse

import utils

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')

if args.strand_specific is not None:
    cmd += ' --strand_specific'
cmd += ' --transcripts %s' % args.transcripts
# Run the command.
utils.run_command(cmd)

54:9a105e8f08e5

#!/usr/bin/env python
import argparse
import os

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_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')

if args.strand_specific is not None:
    cmd += ' --strand_specific'
cmd += ' --transcripts %s' % args.transcripts
# Run the command.
utils.run_command(cmd)

# Handle outputs.
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)