Mercurial > repos > rnateam > viennarna_rnalfold

comparison rnafold_SHAPE.py @ 2:061372702978 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n'
author rnateam
date Tue, 16 May 2017 16:27:48 -0400
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1:05d34c651b11 2:061372702978
1 ### overcoming the problem of SHAPE data working with a single line.
2 ### creating multiple multiple files containg SHAPE data for a single sequence and running RNAfold for every
3 ### single sequence.
4
5 import os
6 import sys
7 from os import system
8 from Bio import SeqIO
9 import re
10 from subprocess import Popen, PIPE
11
12 params_list = sys.argv[1:]
13 param_list_no_shape = [s for s in params_list if not "--shape=" in s ]
14 shape_file = [s for s in params_list if "--shape=" in s ]
15 assert (len(shape_file) == 1)
16
17 shape_file = shape_file[0]
18 shape_file = shape_file.replace('--shape=', '')
19
20 params_no_shape = " ".join(str(x) for x in param_list_no_shape)
21
22 pattern = re.compile("^>.*$")
23 id_line = ""
24 with open(shape_file, 'r') as f:
25 content = f.read()
26 lines = content.split('\n')
27 for line in lines:
28 if pattern.match(line):
29 id_line = line.split()[0]
30 id_line = id_line[1:]
31 continue
32 else:
33 with open(id_line +'.tmp', "a") as clFile:
34 clFile.write(line + "\n")
35
36 input_file = sys.stdin
37
38 for record in SeqIO.parse(input_file, "fasta"):
39 seq = ">{}\n{}".format(record.id,record.seq)
40 cmd = " RNAfold --shape=" + record.id + '.tmp ' + params_no_shape
41 p = Popen(cmd , stdin=PIPE, shell=True, stdout=PIPE, stderr=PIPE)
42 out,err = p.communicate(seq.encode())
43 if err:
44 raise RuntimeError("Error in calling RNAfold\n{}\n{}\n".format(out, err))
45 print (out.decode('utf-8').strip())