Mercurial > repos > artbio > repenrich

comparison RepEnrich_setup.py @ 14:bf866bedd4b4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5
author artbio
date Sat, 20 Apr 2024 12:13:52 +0000
parents 530626b0757c
children 2e3d976e7d5d
comparison
equal deleted inserted replaced
13:530626b0757c 14:bf866bedd4b4
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import csv 3 import csv
4 import os
5 import shlex 4 import shlex
6 import subprocess 5 import subprocess
7 import sys 6 import sys
8 from collections import defaultdict 7 from collections import defaultdict
9 from concurrent.futures import ProcessPoolExecutor 8 from concurrent.futures import ProcessPoolExecutor
45 gapl = args.gaplength 44 gapl = args.gaplength
46 flankingl = args.flankinglength 45 flankingl = args.flankinglength
47 annotation_file = args.annotation_file 46 annotation_file = args.annotation_file
48 genomefasta = args.genomefasta 47 genomefasta = args.genomefasta
49 cpus = args.cpus 48 cpus = args.cpus
50
51 # check that the programs we need are available
52 try:
53 subprocess.call(shlex.split("bowtie --version"),
54 stdout=open(os.devnull, 'wb'),
55 stderr=open(os.devnull, 'wb'))
56 except OSError:
57 print("Error: Bowtie not available in the path")
58 raise
59 49
60 50
61 def starts_with_numerical(list): 51 def starts_with_numerical(list):
62 try: 52 try:
63 if len(list) == 0: 53 if len(list) == 0:
113 metagenome = '' 103 metagenome = ''
114 # iterating coordinate list by block of 3 (chr, start, end) 104 # iterating coordinate list by block of 3 (chr, start, end)
115 block = 3 105 block = 3
116 for i in range(0, len(rep_coords[repname]) - block + 1, block): 106 for i in range(0, len(rep_coords[repname]) - block + 1, block):
117 batch = rep_coords[repname][i:i+block] 107 batch = rep_coords[repname][i:i+block]
118 print(batch)
119 chromosome = batch[0] 108 chromosome = batch[0]
120 start = max(int(batch[1]) - flankingl, 0) 109 start = max(int(batch[1]) - flankingl, 0)
121 end = min(int(batch[2]) + flankingl, 110 end = min(int(batch[2]) + flankingl,
122 int(genome[chromosome]['length'])-1) + 1 111 int(genome[chromosome]['length'])-1) + 1
123 metagenome = ( 112 metagenome = (