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comparison hla_dq.py @ 1:4fc47a3ff9e8 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit 3f631031b57350f0437e90e4de3352725bb84716
author erasmus-medical-center
date Wed, 30 May 2018 09:21:15 -0400
parents 10a407fb5072
children
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0:10a407fb5072 1:4fc47a3ff9e8
40 from A and B, determine possible associated serotypes 40 from A and B, determine possible associated serotypes
41 ''' 41 '''
42 42
43 ''' each combination of DQA1,DQB1,type ''' 43 ''' each combination of DQA1,DQB1,type '''
44 associated_combinations = [ 44 associated_combinations = [
45 ['02:01', '02:02', 'DQ2.2'], 45 ['02:01', '02:02', ' DQ2.2 (02:01-02:02)'],
46 ['03:03', '02:02', 'DQ2.3'], 46 ['03:03', '02:02', ' DQ2.3 (03:03-02:02)'],
47 ['05:01', '02:01', 'DQ2.5'], 47 ['05:01', '02:01', ' DQ2.5 (05:01-02:01)'],
48 ['03:01', '03:02', 'DQ8'], 48 ['03:01', '03:02', ' DQ8 (03:01-03:02)'],
49 ['03:02', '03:02', 'DQ8'], 49 ['03:02', '03:02', ' DQ8 (03:02-03:02)'],
50 ['03:03', '03:02', 'DQ8']] 50 ['03:03', '03:02', ' DQ8 (03:03-03:02)']]
51 51
52 return [a[2] for a in associated_combinations 52 return [a[2] for a in associated_combinations
53 if a[0] in typesA and a[1] in typesB] 53 if a[0] in typesA and a[1] in typesB]
54 54
55 55
81 for line in associations: 81 for line in associations:
82 bcount += 1 82 bcount += 1
83 outfile.write( 83 outfile.write(
84 'A' + str(bcount) + '\t' + 84 'A' + str(bcount) + '\t' +
85 '\t'.join([';'.join(sorted(set(l))) 85 '\t'.join([';'.join(sorted(set(l)))
86 if l else '-' for l in line])+'\n') 86 if l else ' -' for l in line])+'\n')