bogemad

#!/usr/bin/env python

from Bio import SeqIO, bgzf
import sys
from gzip import open as gzopen

infile = sys.argv[1]
outprefix = sys.argv[2]

print("Splitting reads...")

bogemad

#!/usr/bin/env python

import sys, os, re
from Bio import SeqIO

base_dir = sys.argv[1]
keyword = sys.argv[2]
outdir = sys.argv[3]
min_len = int(float(sys.argv[4])*1000000)

bogemad

#!/usr/bin/env python3

import argparse, os, sys, gzip, shutil

parser = argparse.ArgumentParser(description="Reorders and extracts files downloaded using ncbi-genome-download run with the --human-readable option")
parser.add_argument("-o", "--output-directory", required=True, help="Path to the output directory. A directory will be created if one does not exist.", action="store", dest="outdir")
parser.add_argument("-g", "--group-directory", required=True, help="Path to the group (bacteria, viral, etc.) directory from the ncbi-genome-download human-readable output. If refseq genomes were downloaded from the bacteria group then the input should be <ncbi-genome-download-output>/human_readable/refseq/bacteria ", action="store", dest="group_dir")
parser.add_argument("-f", "--force", help="Overwrite files in the output directory.", action='store_true', default=False)
args = parser.parse_args()

bogemad

#!/usr/bin/env python

import os, sys, subprocess

def main():
	conda_base_path = os.path.dirname(os.path.dirname(__file__))
	path = sys.argv[1]
	env = get_env()
	gen_activate_script(path, env, conda_base_path)