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annotate ete_genetree_splitter.py @ 7:6a5282f71f82 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
author earlhaminst
date Thu, 11 Oct 2018 11:52:28 -0400
parents 077021c45b96
children b29ee6a16524
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
earlhaminst
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1 from __future__ import print_function
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
earlhaminst
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3 import optparse
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
earlhaminst
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5 from ete3 import PhyloTree
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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8 def main():
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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9 usage = "usage: %prog --genetree <genetree-file> --speciestree <speciestree-file> [options]"
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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10 parser = optparse.OptionParser(usage=usage)
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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11 parser.add_option('--genetree', help='GeneTree in nhx format')
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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12 parser.add_option('--speciestree', help='Species Tree in nhx format')
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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13 parser.add_option('--species_format', type='int', default=8, help='Species Tree input format (0-9)')
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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14 parser.add_option('--gene_node', type='int', default=0, help='Gene node format 0=gene_species, 1=species_gene')
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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15 parser.add_option('--gainlose', action='store_true', default=False, help='Find out gene gain/lose')
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
earlhaminst
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16 parser.add_option('--output_format', type='int', default=9, help='GeneTree output format (0-9)')
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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17 options, args = parser.parse_args()
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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19 if options.genetree is None:
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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20 parser.error("--genetree option must be specified, GeneTree in nhx format")
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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22 with open(options.genetree, 'r') as f:
6a5282f71f82 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
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23 contents = f.read()
6a5282f71f82 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
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6a5282f71f82 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
earlhaminst
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25 # Remove empty NHX features that can be produced by TreeBest but break ete3
6a5282f71f82 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
earlhaminst
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26 contents = contents.replace('[&&NHX]', '')
6a5282f71f82 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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28 # reads single gene tree
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6a5282f71f82 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
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29 genetree = PhyloTree(contents)
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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31 # sets species naming function
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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32 if options.gene_node == 0:
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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33 genetree.set_species_naming_function(parse_sp_name)
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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35 # reconcile species tree with gene tree to help find out gene gain/lose
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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36 if options.gainlose:
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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38 if options.speciestree is None:
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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39 parser.error("--speciestree option must be specified, species tree in nhx format")
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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41 # reads species tree
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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42 speciestree = PhyloTree(options.speciestree, format=options.species_format)
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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44 # Removes '*' from Species names comes from Species tree configrured for TreeBest
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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45 for leaf in speciestree:
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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46 leaf.name = leaf.name.strip('*')
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48 genetree, events = genetree.reconcile(speciestree)
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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50 # splits tree by duplication events which returns the list of all subtrees resulting from splitting current tree by its duplication nodes.
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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51 for cluster_id, node in enumerate(genetree.split_by_dups(), 1):
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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52 outfile = str(cluster_id) + '_genetree.nhx'
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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53 with open(outfile, 'w') as f:
077021c45b96 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit a22e605b871c2185e98d89598aebb2fa3a82bb8f
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54 f.write(node.write(format=options.output_format))
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57 def parse_sp_name(node_name):
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58 return node_name.split("_")[1]
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61 if __name__ == "__main__":
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62 main()