comparison assembly_post_processor.py @ 49:9d58af3e459d draft

Uploaded

48:564163c7afd8

#!/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')

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)

49:9d58af3e459d

#!/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')

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)