Mercurial > repos > rnateam > viennarna_rnaeval
view rnafold_SHAPE.py @ 7:4f1a37b08904 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
author | rnateam |
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date | Wed, 20 Dec 2017 08:31:22 -0500 |
parents | f9fdedb38919 |
children |
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### overcoming the problem of SHAPE data working with a single line. ### creating multiple multiple files containg SHAPE data for a single sequence and running RNAfold for every ### single sequence. import os import sys from os import system from Bio import SeqIO import re from subprocess import Popen, PIPE params_list = sys.argv[1:] param_list_no_shape = [s for s in params_list if not "--shape=" in s ] shape_file = [s for s in params_list if "--shape=" in s ] assert (len(shape_file) == 1) shape_file = shape_file[0] shape_file = shape_file.replace('--shape=', '') params_no_shape = " ".join(str(x) for x in param_list_no_shape) pattern = re.compile("^>.*$") id_line = "" with open(shape_file, 'r') as f: content = f.read() lines = content.split('\n') for line in lines: if pattern.match(line): id_line = line.split()[0] id_line = id_line[1:] continue else: with open(id_line +'.tmp', "a") as clFile: clFile.write(line + "\n") input_file = sys.stdin for record in SeqIO.parse(input_file, "fasta"): seq = ">{}\n{}".format(record.id,record.seq) cmd = " RNAfold --shape=" + record.id + '.tmp ' + params_no_shape p = Popen(cmd , stdin=PIPE, shell=True, stdout=PIPE, stderr=PIPE) out,err = p.communicate(seq.encode()) if err: raise RuntimeError("Error in calling RNAfold\n{}\n{}\n".format(out, err)) print (out.decode('utf-8').strip())