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annotate ete_gene_cnv.py @ 13:ed74587a13c8 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 23b3c7c09a7d391b576e3b19f8b34dd63d636bdc
author earlhaminst
date Thu, 01 Sep 2022 16:11:32 +0000
parents 16e925bf567e
children
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earlhaminst
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1 from __future__ import print_function
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3 import argparse
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4 import collections
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6 from ete3 import PhyloTree
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9 def printTSV(myDict, colList=None):
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10 """ Pretty print a list of dictionaries (myDict) as a dynamically sized table.
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11 If column names (colList) aren't specified, they will show in random order.
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12 Author: Thierry Husson - Use it as you want but don't blame me.
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13 """
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14 if not colList:
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15 colList = list(myDict[0].keys() if myDict else [])
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17 myList = [colList]
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19 for item in myDict:
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20 myList.append([str(item[col] if item[col] is not None else '') for col in colList])
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22 for item in myList:
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23 print(*item, sep="\t")
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26 def main():
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27 parser = argparse.ArgumentParser(description='Gene Copy Number Finder')
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28 parser.add_argument('--genetree', required=True, help='GeneTree in nhx format')
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29 parser.add_argument('--speciesorder', required=True, help='Comma-separated species list')
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30 args = parser.parse_args()
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32 species_list = args.speciesorder.split(",")
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33 species_list = [_.strip() for _ in species_list]
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34 table = []
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36 with open(args.genetree, "r") as f:
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37 # reads multiple gene tree line by line gene tree
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38 for line in f:
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39 # Remove empty NHX features that can be produced by TreeBest but break ete3
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40 line = line.replace('[&&NHX]', '')
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42 # reads single gene tree
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43 genetree = PhyloTree(line)
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44 leaves = genetree.get_leaf_names()
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46 leaves_parts = [_.split("_") for _ in leaves]
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47 for i, leaf_parts in enumerate(leaves_parts):
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48 if len(leaf_parts) < 2:
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49 raise Exception("Leaf node '%s' is not in gene_species format" % leaves[i])
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50
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51 leaves_species = [_[-1] for _ in leaves_parts]
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52 species_counter = collections.Counter(leaves_species)
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54 # Assign to ref_species the first element of species_list which
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55 # appears in a leaf node
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56 for ref_species in species_list:
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57 if ref_species in species_counter:
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58 break
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59 else:
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60 raise Exception("None of the specified species was found in the GeneTree '%s'" % line)
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62 # Find the gene of the (first) leaf node for the ref_species
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63 for leaf_parts in leaves_parts:
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64 if leaf_parts[-1] == ref_species:
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65 species_counter['gene'] = "_".join(leaf_parts[:-1])
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66 break
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68 table.append(species_counter)
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70 colList = ["gene"] + species_list
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71 printTSV(table, colList)
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74 if __name__ == "__main__":
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75 main()