comparison RepEnrich.py @ 14:bf866bedd4b4 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5

13:530626b0757c

import argparse
import csv
import os
import shlex
import subprocess
import sys
from collections import defaultdict
from concurrent.futures import ProcessPoolExecutor

simple_repeat = "Simple_repeat"
if args.fastqfile2:
    paired_end = True
else:
    paired_end = False

# check that the programs we need are available
try:
    subprocess.call(shlex.split("coverageBed -h"),
                    stdout=open(os.devnull, 'wb'),
                    stderr=open(os.devnull, 'wb'))
    subprocess.call(shlex.split("bowtie --version"),
                    stdout=open(os.devnull, 'wb'),
                    stderr=open(os.devnull, 'wb'))
except OSError:
    print("Error: Bowtie or bedtools not loaded")
    raise


def starts_with_numerical(list):
    try:
        if len(list) == 0:

14:bf866bedd4b4

import argparse
import csv
import shlex
import subprocess
import sys
from collections import defaultdict
from concurrent.futures import ProcessPoolExecutor

simple_repeat = "Simple_repeat"
if args.fastqfile2:
    paired_end = True
else:
    paired_end = False


def starts_with_numerical(list):
    try:
        if len(list) == 0: