Mercurial > repos > rnateam > viennarna_kinwalker

annotate rnafold_SHAPE.py @ 0:5bfbb403c175 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author rnateam
date Wed, 12 Jul 2017 14:16:22 -0400
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5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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diff changeset
1 ### overcoming the problem of SHAPE data working with a single line.
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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2 ### creating multiple multiple files containg SHAPE data for a single sequence and running RNAfold for every
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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3 ### single sequence.
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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5 import os
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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6 import sys
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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7 from os import system
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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8 from Bio import SeqIO
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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9 import re
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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10 from subprocess import Popen, PIPE
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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11
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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12 params_list = sys.argv[1:]
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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13 param_list_no_shape = [s for s in params_list if not "--shape=" in s ]
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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14 shape_file = [s for s in params_list if "--shape=" in s ]
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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15 assert (len(shape_file) == 1)
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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17 shape_file = shape_file[0]
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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18 shape_file = shape_file.replace('--shape=', '')
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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20 params_no_shape = " ".join(str(x) for x in param_list_no_shape)
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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22 pattern = re.compile("^>.*$")
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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23 id_line = ""
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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24 with open(shape_file, 'r') as f:
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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25 content = f.read()
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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26 lines = content.split('\n')
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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27 for line in lines:
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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28 if pattern.match(line):
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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29 id_line = line.split()[0]
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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30 id_line = id_line[1:]
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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31 continue
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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32 else:
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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33 with open(id_line +'.tmp', "a") as clFile:
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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34 clFile.write(line + "\n")
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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36 input_file = sys.stdin
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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37
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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38 for record in SeqIO.parse(input_file, "fasta"):
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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39 seq = ">{}\n{}".format(record.id,record.seq)
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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40 cmd = " RNAfold --shape=" + record.id + '.tmp ' + params_no_shape
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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41 p = Popen(cmd , stdin=PIPE, shell=True, stdout=PIPE, stderr=PIPE)
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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42 out,err = p.communicate(seq.encode())
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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43 if err:
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
rnateam
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44 raise RuntimeError("Error in calling RNAfold\n{}\n{}\n".format(out, err))
5bfbb403c175 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
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45 print (out.decode('utf-8').strip())