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annotate fasta_concatenate_by_species.py @ 3:49e91b42881b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit 34a6c9f94a5722bb7d2f887618aafa410a770e91"
author devteam
date Mon, 02 Mar 2020 11:46:08 +0000
parents c5311b7718d1
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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
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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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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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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9 import sys
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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10 import tempfile
c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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11 from collections import OrderedDict
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13 from utils.maf_utilities import iter_fasta_alignment
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15
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16 def __main__():
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17 input_filename = sys.argv[1]
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18 output_filename = sys.argv[2]
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19 species = OrderedDict()
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20 cur_size = 0
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c5311b7718d1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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21 for components in iter_fasta_alignment(input_filename):
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22 species_not_written = list(species.keys())
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23 for component in components:
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24 if component.species not in species:
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25 species[component.species] = tempfile.TemporaryFile(mode="r+")
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26 species[component.species].write("-" * cur_size)
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27 species[component.species].write(component.text)
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28 try:
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29 species_not_written.remove(component.species)
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30 except ValueError:
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31 # this is a new species
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32 pass
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33 for spec in species_not_written:
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34 species[spec].write("-" * len(components[0].text))
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35 cur_size += len(components[0].text)
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36 with open(output_filename, 'w') as out:
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37 for spec, f in species.items():
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38 f.seek(0)
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39 out.write(">%s\n%s\n" % (spec, f.read()))
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42 if __name__ == "__main__":
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43 __main__()