Mercurial > repos > rnateam > rnacommender

annotate fasta_utils/__init__.py @ 0:d04fa5201f51 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
author rnateam
date Thu, 28 Jul 2016 05:56:54 -0400
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d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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1 """Util functions for FASTA format."""
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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2
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3 __author__ = "Gianluca Corrado"
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4 __copyright__ = "Copyright 2016, Gianluca Corrado"
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5 __license__ = "MIT"
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6 __maintainer__ = "Gianluca Corrado"
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7 __email__ = "gianluca.corrado@unitn.it"
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8 __status__ = "Production"
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11 def import_fasta(fasta_file):
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12 """Import a fasta file as a dictionary."""
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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13 dic = {}
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14 f = open(fasta_file)
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15 fasta = f.read().strip()
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16 f.close()
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17 for a in fasta.split('>'):
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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18 k = a.split('\n')[0]
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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19 v = ''.join(a.split('\n')[1:])
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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20 if k != '':
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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21 dic[k] = v
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22 return dic
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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25 def export_fasta(dic):
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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26 """Export a dictionary."""
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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27 fasta = ""
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28 for (k, v) in dic.iteritems():
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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29 fasta += ">%s\n%s\n" % (k, v)
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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30 return fasta
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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33 def seq_names(fasta_file):
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34 """Get sequence names from fasta file."""
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35 names = []
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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36 f = open(fasta_file)
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37 fasta = f.read()
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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38 f.close()
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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39 for a in fasta.split('>'):
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40 names.append(a.split('\n')[0])
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41 return [a for a in names if a != '']
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42
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43
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44 def stockholm2fasta(stockholm):
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45 """Convert alignment in stockholm format to fasta format."""
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46 fasta = ""
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47 for line in stockholm.split("\n"):
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48 # comment line
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49 if line[0] == "#":
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50 continue
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51 # termination line
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52 elif line == "//":
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53 return fasta
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54 # alignment line
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55 else:
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56 name, align = line.split()
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57 seq = align.replace(".", "")
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58 fasta += ">%s\n%s\n" % (name, seq)