Mercurial > repos > artbio > repenrich
comparison RepEnrich.py @ 14:bf866bedd4b4 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5
author | artbio |
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date | Sat, 20 Apr 2024 12:13:52 +0000 |
parents | 530626b0757c |
children |
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13:530626b0757c | 14:bf866bedd4b4 |
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1 import argparse | 1 import argparse |
2 import csv | 2 import csv |
3 import os | |
4 import shlex | 3 import shlex |
5 import subprocess | 4 import subprocess |
6 import sys | 5 import sys |
7 from collections import defaultdict | 6 from collections import defaultdict |
8 from concurrent.futures import ProcessPoolExecutor | 7 from concurrent.futures import ProcessPoolExecutor |
43 simple_repeat = "Simple_repeat" | 42 simple_repeat = "Simple_repeat" |
44 if args.fastqfile2: | 43 if args.fastqfile2: |
45 paired_end = True | 44 paired_end = True |
46 else: | 45 else: |
47 paired_end = False | 46 paired_end = False |
48 | |
49 # check that the programs we need are available | |
50 try: | |
51 subprocess.call(shlex.split("coverageBed -h"), | |
52 stdout=open(os.devnull, 'wb'), | |
53 stderr=open(os.devnull, 'wb')) | |
54 subprocess.call(shlex.split("bowtie --version"), | |
55 stdout=open(os.devnull, 'wb'), | |
56 stderr=open(os.devnull, 'wb')) | |
57 except OSError: | |
58 print("Error: Bowtie or bedtools not loaded") | |
59 raise | |
60 | 47 |
61 | 48 |
62 def starts_with_numerical(list): | 49 def starts_with_numerical(list): |
63 try: | 50 try: |
64 if len(list) == 0: | 51 if len(list) == 0: |