annotate gemini_mafify.py @ 7:2969a1f43b7d draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
author iuc
date Tue, 10 Mar 2020 06:15:27 -0400
parents
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7
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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1 import string
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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2 import sys
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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3
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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4
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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5 so_to_maf = {
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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6 'splice_acceptor_variant': 'Splice_Site',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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7 'splice_donor_variant': 'Splice_Site',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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8 'transcript_ablation': 'Splice_Site',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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9 'exon_loss_variant': 'Splice_Site',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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10 'stop_gained': 'Nonsense_Mutation',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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11 'stop_lost': 'Nonstop_Mutation',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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12 'frameshift_variant': 'Frame_Shift_',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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13 'initiator_codon_variant': 'Translation_Start_Site',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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14 'start_lost': 'Translation_Start_Site',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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15 'inframe_insertion': 'In_Frame_Ins',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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16 'inframe_deletion': 'In_Frame_Del',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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17 'conservative_inframe_insertion': 'In_Frame_Ins',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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18 'conservative_inframe_deletion': 'In_Frame_Del',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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19 'disruptive_inframe_insertion': 'In_Frame_Ins',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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20 'disruptive_inframe_deletion': 'In_Frame_Del',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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21 'missense_variant': 'Missense_Mutation',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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22 'coding_sequence_variant': 'Missense_Mutation',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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23 'conservative_missense_variant': 'Missense_Mutation',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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24 'rare_amino_acid_variant': 'Missense_Mutation',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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25 'transcript_amplification': 'Intron',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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26 'intron_variant': 'Intron',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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27 'INTRAGENIC': 'Intron',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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28 'intragenic_variant': 'Intron',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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29 'splice_region_variant': 'Splice_Region',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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30 'mature_miRNA_variant': 'RNA',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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31 'exon_variant': 'RNA',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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32 'non_coding_exon_variant': 'RNA',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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33 'non_coding_transcript_exon_variant': 'RNA',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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34 'non_coding_transcript_variant': 'RNA',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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35 'nc_transcript_variant': 'RNA',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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36 'stop_retained_variant': 'Silent',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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37 'synonymous_variant': 'Silent',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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38 'NMD_transcript_variant': 'Silent',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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39 'incomplete_terminal_codon_variant': 'Silent',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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40 '5_prime_UTR_variant': "5'UTR",
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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41 '5_prime_UTR_premature_start_codon_gain_variant': "5'UTR",
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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42 '3_prime_UTR_variant': "3'UTR",
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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43 'intergenic_variant': 'IGR',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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44 'intergenic_region': 'IGR',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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45 'regulatory_region_variant': 'IGR',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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46 'regulatory_region': 'IGR',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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47 'TF_binding_site_variant': 'IGR',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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48 'upstream_gene_variant': "5'Flank",
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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49 'downstream_gene_variant': "3'Flank",
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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50 }
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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51
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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52
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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53 class VariantEffect():
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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54 def __init__(self, variant_type):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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55 self.variant_type = variant_type.capitalize()
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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56 assert self.variant_type in ['Snp', 'Ins', 'Del']
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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57
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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58 def __getitem__(self, so_effect):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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59 if so_effect not in so_to_maf or (
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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60 'frame' in so_effect and self.variant_type == 'Snp'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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61 ):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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62 return 'Targeted_Region'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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63
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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64 ret = so_to_maf[so_effect]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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65 if ret == 'Frame_Shift_':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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66 ret += self.variant_type
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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67 return ret
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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68
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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69
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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70 infile = sys.argv[1]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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71 if len(sys.argv) > 2:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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72 tumor_sample_name = sys.argv[2]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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73 if len(sys.argv) > 3:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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74 normal_sample_name = sys.argv[3]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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75
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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76 start_pos_idx = None
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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77 ref_idx = None
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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78 alt_idx = None
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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79 variant_type_idx = None
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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80 variant_classification_idx = None
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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81 gt_alt_depths_idx = {}
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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82 gt_ref_depths_idx = {}
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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diff changeset
83 gts_idx = {}
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
84 samples = set()
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
85 required_fields = [
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
86 'Hugo_Symbol',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
87 'NCBI_Build',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
88 'Variant_Type',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
89 'Variant_Classification',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
90 'Tumor_Sample_Barcode',
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
91 'HGVSp_Short'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
92 ]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
93
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
94
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
95 with open(infile) as data_in:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
96 cols = data_in.readline().rstrip().split('\t')
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
97 for field in required_fields:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
98 if field not in cols:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
99 raise IndexError(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
100 'Cannot generate valid MAF without the following input '
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
101 'columns: {0}.\n'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
102 'Missing column: "{1}"'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
103 .format(required_fields, field)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
104 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
105 for i, col in enumerate(cols):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
106 if col == 'Variant_Type':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
107 variant_type_idx = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
108 elif col == 'Variant_Classification':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
109 variant_classification_idx = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
110 elif col == 'Start_Position':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
111 start_pos_idx = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
112 elif col == 'Reference_Allele':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
113 ref_idx = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
114 elif col == 'alt':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
115 alt_idx = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
116 else:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
117 column, _, sample = col.partition('.')
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
118 if sample:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
119 if column == 'gt_alt_depths':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
120 gt_alt_depths_idx[sample] = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
121 elif column == 'gt_ref_depths':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
122 gt_ref_depths_idx[sample] = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
123 elif column == 'gts':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
124 gts_idx[sample] = i
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
125 else:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
126 # not a recognized sample-specific column
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
127 continue
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
128 samples.add(sample)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
129
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
130 if ref_idx is None:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
131 raise IndexError('Input file does not have a column "Reference_Allele".')
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
132
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
133 if not tumor_sample_name:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
134 if normal_sample_name:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
135 raise ValueError(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
136 'Normal sample name requires the tumor sample name to be '
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
137 'specified, too.'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
138 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
139 if len(samples) > 1:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
140 raise ValueError(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
141 'A tumor sample name is required with more than one sample '
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
142 'in the input.'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
143 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
144 if samples:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
145 # There is a single sample with genotype data.
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
146 # Assume its the tumor sample.
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
147 tumor_sample_name = next(iter(samples))
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
148 else:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
149 if tumor_sample_name not in samples:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
150 raise ValueError(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
151 'Could not find information about the specified tumor sample '
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
152 'in the input.'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
153 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
154 if tumor_sample_name == normal_sample_name:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
155 raise ValueError(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
156 'Need different names for the normal and the tumor sample.'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
157 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
158
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
159 if normal_sample_name and normal_sample_name not in samples:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
160 raise ValueError(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
161 'Could not find information about the specified normal sample '
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
162 'in the input.'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
163 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
164
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
165 # All input data checks passed!
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
166 # Now extract just the relevant index numbers for the tumor/normal pair
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
167 gts_idx = (
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
168 gts_idx.get(tumor_sample_name, alt_idx),
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
169 gts_idx.get(normal_sample_name)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
170 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
171 gt_alt_depths_idx = (
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
172 gt_alt_depths_idx.get(tumor_sample_name),
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
173 gt_alt_depths_idx.get(normal_sample_name)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
174 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
175 gt_ref_depths_idx = (
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
176 gt_ref_depths_idx.get(tumor_sample_name),
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
177 gt_ref_depths_idx.get(normal_sample_name)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
178 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
179
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
180 # Echo all MAF column names
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
181 cols_to_print = []
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
182 for n in range(len(cols)):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
183 if n in gts_idx:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
184 continue
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
185 if n in gt_alt_depths_idx:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
186 continue
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
187 if n in gt_ref_depths_idx:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
188 continue
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
189 if n != alt_idx:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
190 cols_to_print.append(n)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
191
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
192 print('\t'.join([cols[n] for n in cols_to_print]))
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
193
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
194 for line in data_in:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
195 cols = line.rstrip().split('\t')
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
196
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
197 gt_alt_depths = [
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
198 int(cols[ad_idx]) if ad_idx else ''
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
199 for ad_idx in gt_alt_depths_idx
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
200 ]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
201 gt_ref_depths = [
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
202 int(cols[rd_idx]) if rd_idx else ''
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
203 for rd_idx in gt_ref_depths_idx
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
204 ]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
205
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
206 gts = [
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
207 ['', ''],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
208 ['', '']
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
209 ]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
210 for n, gt_idx in enumerate(gts_idx):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
211 if gt_idx:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
212 gt_sep = '/' if '/' in cols[gt_idx] else '|'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
213 allele1, _, allele2 = [
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
214 '' if allele == '.' else allele
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
215 for allele in cols[gt_idx].partition(gt_sep)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
216 ]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
217 # follow cBioportal recommendation to leave allele1 empty
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
218 # when information is not avaliable
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
219 if not allele2:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
220 gts[n] = [allele2, allele1]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
221 else:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
222 gts[n] = [allele1, allele2]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
223 if not gts:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
224 gts = [['', ''], ['', '']]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
225
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
226 if cols[variant_type_idx].lower() in ['ins', 'del']:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
227 # transform VCF-style indel representations into MAF ones
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
228 ref_allele = cols[ref_idx]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
229 for n, nucs in enumerate(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
230 zip(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
231 ref_allele,
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
232 *[allele for gt in gts for allele in gt if allele]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
233 )
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
234 ):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
235 if any(nuc != nucs[0] for nuc in nucs[1:]):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
236 break
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
237 else:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
238 n += 1
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
239 if n > 0:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
240 cols[ref_idx] = cols[ref_idx][n:] or '-'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
241 for gt in gts:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
242 for idx, allele in enumerate(gt):
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
243 if allele:
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
244 gt[idx] = allele[n:] or '-'
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
245 if cols[ref_idx] == '-':
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
246 n -= 1
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
247 cols[start_pos_idx] = str(int(cols[start_pos_idx]) + n)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
248
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
249 # in-place substitution of so_effect with MAF effect
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
250 cols[variant_classification_idx] = VariantEffect(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
251 cols[variant_type_idx]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
252 )[cols[variant_classification_idx]]
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
253 ret_line = '\t'.join([cols[n] for n in cols_to_print])
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
254
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
255 field_formatters = {
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
256 'tumor_seq_allele1': gts[0][0],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents:
diff changeset
257 'tumor_seq_allele2': gts[0][1],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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258 'match_norm_seq_allele1': gts[1][0],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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259 'match_norm_seq_allele2': gts[1][1],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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260 't_alt_count': gt_alt_depths[0],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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261 'n_alt_count': gt_alt_depths[1],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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262 't_ref_count': gt_ref_depths[0],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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263 'n_ref_count': gt_ref_depths[1],
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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264 }
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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265
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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266 print(
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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267 # use safe_substitute here to avoid key errors with column content
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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268 # looking like unknown placeholders
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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269 string.Template(ret_line).safe_substitute(field_formatters)
2969a1f43b7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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270 )