rna_download_rfam.get_parser() - Code Metrics - Inspection of "rna_tools/tools/rna_rfam/rna_download_rfam.py" - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

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by Marcin

created 2024-12-29 16:25 UTC

rna_download_rfam.get_parser() A

↳ Parent: rna_download_rfam

Complexity

Conditions

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Total Lines	10
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	7
nop	0
dl	0
loc	10
rs	10
c	0
b	0
f	0

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""rna_download_rfam.py - download all cm and seeds

For the list grep seed file::

    (base) rnahub@rnahub:~/db/rfam$ grep '#=GF AC' Rfam.seed  | wc -l
    #=GF AC   RF04297
    #=GF AC   RF04298
    #=GF AC   RF04299
    #=GF AC   RF04300

or cm::

    (base) rnahub@rnahub:~/db/rfam$ grep ACC Rfam.cm
    ACC      RF04235
    ACC   RF04235
    ACC      RF04236
    ACC   RF04236


"""
from __future__ import print_function
import argparse
from icecream import ic
import sys
ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
ic.configureOutput(prefix='> ')
import os

def process_rfam(family_id, job_path='./rfam'):
        os.system(f"wget https://rfam.org/family/{family_id}/alignment/stockholm -O  {job_path}/{family_id}.seed.sto")
        os.system(f"wget https://rfam.org/family/{family_id}/alignment/fastau -O {job_path}/{family_id}.seed.fa")
        os.system(f"wget https://rfam.org/family/{family_id}/cm -O {job_path}/{family_id}.cm")

def get_parser():
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    #parser.add_argument('-', "--", help="", default="")

    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    parser.add_argument("file", help="", default="") # nargs='+')
    return parser


if __name__ == '__main__':
    parser = get_parser()
    args = parser.parse_args()

    for l in open(args.file):
        rfam_id = l.split()[2]
        print(rfam_id)
        process_rfam(rfam_id)


1			#!/usr/bin/env python
2			# -- coding: utf-8 --
3			"""rna_download_rfam.py - download all cm and seeds
4
5			For the list grep seed file::
6
7			(base) rnahub@rnahub:~/db/rfam$ grep '#=GF AC' Rfam.seed \| wc -l
8			#=GF AC RF04297
9			#=GF AC RF04298
10			#=GF AC RF04299
11			#=GF AC RF04300
12
13			or cm::
14
15			(base) rnahub@rnahub:~/db/rfam$ grep ACC Rfam.cm
16			ACC RF04235
17			ACC RF04235
18			ACC RF04236
19			ACC RF04236
20
21
22			"""
23			from __future__ import print_function
24			import argparse
25			from icecream import ic
26			import sys
27			ic.configureOutput(outputFunction=lambda a: print(a, file=sys.stderr))
28			ic.configureOutput(prefix='> ')
29			import os
30
31			def process_rfam(family_id, job_path='./rfam'):
32			os.system(f"wget https://rfam.org/family/{family_id}/alignment/stockholm -O {job_path}/{family_id}.seed.sto")
33			os.system(f"wget https://rfam.org/family/{family_id}/alignment/fastau -O {job_path}/{family_id}.seed.fa")
34			os.system(f"wget https://rfam.org/family/{family_id}/cm -O {job_path}/{family_id}.cm")
35
36			def get_parser():
37			parser = argparse.ArgumentParser(
38			description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
39
40			#parser.add_argument('-', "--", help="", default="")
41
42			parser.add_argument("-v", "--verbose",
43			action="store_true", help="be verbose")
44			parser.add_argument("file", help="", default="") # nargs='+')
45			return parser
46
47
48			if __name__ == '__main__':
49			parser = get_parser()
50			args = parser.parse_args()
51
52			for l in open(args.file):
53			rfam_id = l.split()[2]
54			print(rfam_id)
55			process_rfam(rfam_id)
56

mmagnus / rna-tools

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rna_download_rfam.get_parser() A

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