comparison RepEnrich_setup.py @ 14:bf866bedd4b4 draft

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

13:530626b0757c

#!/usr/bin/env python
import argparse
import csv
import os
import shlex
import subprocess
import sys
from collections import defaultdict
from concurrent.futures import ProcessPoolExecutor

gapl = args.gaplength
flankingl = args.flankinglength
annotation_file = args.annotation_file
genomefasta = args.genomefasta
cpus = args.cpus

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


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

    metagenome = ''
    # iterating coordinate list by block of 3 (chr, start, end)
    block = 3
    for i in range(0, len(rep_coords[repname]) - block + 1, block):
        batch = rep_coords[repname][i:i+block]
        print(batch)
        chromosome = batch[0]
        start = max(int(batch[1]) - flankingl, 0)
        end = min(int(batch[2]) + flankingl,
                  int(genome[chromosome]['length'])-1) + 1
        metagenome = (

14:bf866bedd4b4

#!/usr/bin/env python
import argparse
import csv
import shlex
import subprocess
import sys
from collections import defaultdict
from concurrent.futures import ProcessPoolExecutor

gapl = args.gaplength
flankingl = args.flankinglength
annotation_file = args.annotation_file
genomefasta = args.genomefasta
cpus = args.cpus


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

    metagenome = ''
    # iterating coordinate list by block of 3 (chr, start, end)
    block = 3
    for i in range(0, len(rep_coords[repname]) - block + 1, block):
        batch = rep_coords[repname][i:i+block]
        chromosome = batch[0]
        start = max(int(batch[1]) - flankingl, 0)
        end = min(int(batch[2]) + flankingl,
                  int(genome[chromosome]['length'])-1) + 1
        metagenome = (