Mercurial > repos > erasmus-medical-center > hla_dq

annotate 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
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10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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1 #!/usr/bin/env python
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2 '''
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3 Given HLA-A and HLA-B genes annotated with BLAST IMGT/HLA database
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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4 genotypes, determine associated serotypes
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7 DQA1 | DQB1 | type
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8 --------------------
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9 02:01| 02:02| DQ2.2
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10 03:03| 02:02| DQ2.3
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11 05:01| 02:01| DQ2.3
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12 03:01| 03:02| DQ8
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13 03:02| 03:02| DQ8
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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14 03:03| 03:02| DQ8
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16 Annotations are of form DQ[A|B]1*xx:yy[:zz[:vv]] where xx:yy is of interest.
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18 Example: "HLA:HLA11066 DQA1*01:05:02 768 bp"
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19 '''
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21 import argparse
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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22 import itertools
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25 def to_matrix(l, n):
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26 return [l[i:i+n] for i in range(0, len(l), n)]
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29 def get_list_of_associated_types(filename, column):
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30 with open(filename) as f:
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31 contents = f.readlines()
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33 return [':'.join(line.split('\t')[column-1].split(' ')[1]
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34 .split('*')[1].split(':')[0:2])
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35 for line in contents[1:]]
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38 def get_associations(typesA, typesB):
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39 ''' Given list of genotype annotations (e.g. DQA1*02:01..)
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40 from A and B, determine possible associated serotypes
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41 '''
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43 ''' each combination of DQA1,DQB1,type '''
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44 associated_combinations = [
1
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45 ['02:01', '02:02', ' DQ2.2 (02:01-02:02)'],
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46 ['03:03', '02:02', ' DQ2.3 (03:03-02:02)'],
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47 ['05:01', '02:01', ' DQ2.5 (05:01-02:01)'],
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48 ['03:01', '03:02', ' DQ8 (03:01-03:02)'],
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49 ['03:02', '03:02', ' DQ8 (03:02-03:02)'],
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50 ['03:03', '03:02', ' DQ8 (03:03-03:02)']]
0
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52 return [a[2] for a in associated_combinations
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53 if a[0] in typesA and a[1] in typesB]
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56 if __name__ == "__main__":
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57 parser = argparse.ArgumentParser()
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58 parser.add_argument('-A', required=True, action='append',
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59 help='BLAST hits A gene')
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60 parser.add_argument('-B', required=True, action='append',
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61 help='BLAST hits B gene')
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62 parser.add_argument('-c', '--column', default=5, type=int,
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63 help='Column number containing the BLAST annotation')
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64 args = parser.parse_args()
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65
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66 # TODO: QC check that file A contains DQA1 annotations and
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67 # B file contains DQB1 annotations?
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68
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69 # find possible associated types, for all combinations of alleles
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70 typesA = [get_list_of_associated_types(A, args.column) for A in args.A]
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71 typesB = [get_list_of_associated_types(B, args.column) for B in args.B]
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72 associations = [get_associations(c[0], c[1])
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73 for c in itertools.product(typesA, typesB)]
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74 associations = to_matrix(associations, len(args.B))
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75
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76 # write output table
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77 header = '\t'+'\t'.join(['B'+str(i+1) for i in range(0, len(args.B))])+'\n'
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
78 bcount = 0
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
79 with open('results.tsv', 'w') as outfile:
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
80 outfile.write(header)
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
81 for line in associations:
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
82 bcount += 1
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
83 outfile.write(
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
84 'A' + str(bcount) + '\t' +
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
parents:
diff changeset
85 '\t'.join([';'.join(sorted(set(l)))
1
4fc47a3ff9e8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit 3f631031b57350f0437e90e4de3352725bb84716
erasmus-medical-center
parents: 0
diff changeset
86 if l else ' -' for l in line])+'\n')