rna_download_rfam

Complexity

Total Complexity

2

Size/Duplication

Total Lines	56
Duplicated Lines	0 %

Importance

Changes

0

2 Functions

Rating	Name	Duplication	Size	Complexity
A	process_rfam()	0	4	1
A	get_parser()	0	10	1

#!/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)