Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/fasta_concatenate_by_species.py @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 """
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4 Takes a Multiple Alignment FASTA file and concatenates
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 sequences for each species, resulting in one sequence
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6 alignment per species.
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7 """
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8
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9 import sys, tempfile
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10 from galaxy import eggs
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11 from galaxy.tools.util.maf_utilities import iter_fasta_alignment
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12 from galaxy.util.odict import odict
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13
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14 def __main__():
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15 input_filename = sys.argv[1]
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16 output_filename = sys.argv[2]
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17 species = odict()
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18 cur_size = 0
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19 for components in iter_fasta_alignment( input_filename ):
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20 species_not_written = species.keys()
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21 for component in components:
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22 if component.species not in species:
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23 species[component.species] = tempfile.TemporaryFile()
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24 species[component.species].write( "-" * cur_size )
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25 species[component.species].write( component.text )
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26 try:
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27 species_not_written.remove( component.species )
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28 except ValueError:
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29 #this is a new species
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30 pass
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31 for spec in species_not_written:
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32 species[spec].write( "-" * len( components[0].text ) )
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33 cur_size += len( components[0].text )
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34 out = open( output_filename, 'wb' )
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35 for spec, f in species.iteritems():
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36 f.seek( 0 )
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37 out.write( ">%s\n%s\n" % ( spec, f.read() ) )
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38 out.close()
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39
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40 if __name__ == "__main__" : __main__()