Mercurial > repos > earlhaminst > ete
annotate ete_species_tree_generator.py @ 3:077021c45b96 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
author | earlhaminst |
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date | Mon, 12 Mar 2018 12:51:48 -0400 |
parents | 03c10736e497 |
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rev | line source |
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a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
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1 import optparse |
2
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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2 import sys |
1
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
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3 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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4 from ete3 import NCBITaxa |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
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5 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
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6 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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7 parser = optparse.OptionParser() |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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8 parser.add_option('-s', '--species', dest="input_species_filename", |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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9 help='Species list in text format one species in each line') |
2
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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10 parser.add_option('-d', '--database', dest="database", default=None, |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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11 help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)') |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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12 parser.add_option('-o', '--output', dest="output", help='output file name (default: stdout)') |
1
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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13 parser.add_option('-f', '--format', type='choice', choices=['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '100'], dest="format", |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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14 default='8', help='outpur format for tree') |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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15 parser.add_option('-t', '--treebest', type='choice', choices=['yes', 'no'], dest="treebest", |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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16 default='no', help='To be used in TreeBest') |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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17 options, args = parser.parse_args() |
2
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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18 if options.input_species_filename is None: |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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19 parser.error("-s option must be specified, Species list in text format one species in each line") |
1
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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20 |
2
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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21 ncbi = NCBITaxa(dbfile=options.database) |
1
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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22 with open(options.input_species_filename) as f: |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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23 species_name = [_.strip().replace('_', ' ') for _ in f.readlines()] |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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24 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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25 name2taxid = ncbi.get_name_translator(species_name) |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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26 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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27 taxid = [name2taxid[_][0] for _ in species_name] |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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28 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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29 tree = ncbi.get_topology(taxid) |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
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30 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
|
31 if options.treebest == "yes": |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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32 inv_map = {str(v[0]): k.replace(" ", "") + "*" for k, v in name2taxid.items()} |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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33 else: |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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34 inv_map = {str(v[0]): k for k, v in name2taxid.items()} |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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35 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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36 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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37 for leaf in tree: |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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38 leaf.name = inv_map[leaf.name] |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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39 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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40 newickTree = tree.write(format=int(options.format)) |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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41 |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
|
42 if options.treebest == "yes": |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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43 newickTree = newickTree.rstrip(';') |
a4ba317fc713
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit df73a2add6dba8550867034e157ed0699b3b2f53
earlhaminst
parents:
diff
changeset
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44 newickTree = newickTree + "root;" |
2
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
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45 # setup output |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
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46 if not options.output: # if filename is not given |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
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47 of = sys.stdout |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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48 else: |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
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49 of = open(options.output, "w") |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
changeset
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50 of.write(newickTree) |
03c10736e497
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
1
diff
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51 of.close() |