Mercurial > repos > earlhaminst > ete

comparison ete_homology_classifier.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 f1eca1158f21
children
comparison
equal deleted inserted replaced
12:dc32007a6b36 13:ed74587a13c8
27 27
28 leaves_list = genetree.get_leaf_names() 28 leaves_list = genetree.get_leaf_names()
29 # Genetree nodes are required to be in gene_species format 29 # Genetree nodes are required to be in gene_species format
30 leaves_list = [_ for _ in leaves_list if '_' in _] 30 leaves_list = [_ for _ in leaves_list if '_' in _]
31 31
32 species_list = [_.split("_")[1] for _ in leaves_list] 32 species_list = [_.split("_")[-1] for _ in leaves_list]
33 33
34 species_dict = {} 34 species_dict = {}
35 for species in species_list: 35 for species in species_list:
36 count = "one" 36 count = "one"
37 if species in species_dict: 37 if species in species_dict:
49 # stores relevant homology types in dict 49 # stores relevant homology types in dict
50 for i, leaf1 in enumerate(leaves_list): 50 for i, leaf1 in enumerate(leaves_list):
51 for leaf2 in leaves_list[i + 1:]: 51 for leaf2 in leaves_list[i + 1:]:
52 id1 = leaf1.split(":")[1] if ":" in leaf1 else leaf1 52 id1 = leaf1.split(":")[1] if ":" in leaf1 else leaf1
53 id2 = leaf2.split(":")[1] if ":" in leaf2 else leaf2 53 id2 = leaf2.split(":")[1] if ":" in leaf2 else leaf2
54 species1 = id1.split("_")[1] 54 species1 = id1.split("_")[-1]
55 species2 = id2.split("_")[1] 55 species2 = id2.split("_")[-1]
56 if species1 == species2: 56 if species1 == species2:
57 homology_type = 'paralogs' 57 homology_type = 'paralogs'
58 else: 58 else:
59 homology_type = species_dict[species1] + "-to-" + species_dict[species2] 59 homology_type = species_dict[species1] + "-to-" + species_dict[species2]
60 homologies[homology_type].append((id1, id2)) 60 homologies[homology_type].append((id1, id2))