Mercurial > repos > iuc > gemini_db_info
changeset 7:7d75673f4d6f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 06:20:59 -0400 |
| parents | 496124e09f82 |
| children | c2a413e47fe9 |
| files | gemini_mafify.py test-data/gemini_query_as_maf_result.tabular |
| diffstat | 2 files changed, 309 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gemini_mafify.py Tue Mar 10 06:20:59 2020 -0400 @@ -0,0 +1,270 @@ +import string +import sys + + +so_to_maf = { + 'splice_acceptor_variant': 'Splice_Site', + 'splice_donor_variant': 'Splice_Site', + 'transcript_ablation': 'Splice_Site', + 'exon_loss_variant': 'Splice_Site', + 'stop_gained': 'Nonsense_Mutation', + 'stop_lost': 'Nonstop_Mutation', + 'frameshift_variant': 'Frame_Shift_', + 'initiator_codon_variant': 'Translation_Start_Site', + 'start_lost': 'Translation_Start_Site', + 'inframe_insertion': 'In_Frame_Ins', + 'inframe_deletion': 'In_Frame_Del', + 'conservative_inframe_insertion': 'In_Frame_Ins', + 'conservative_inframe_deletion': 'In_Frame_Del', + 'disruptive_inframe_insertion': 'In_Frame_Ins', + 'disruptive_inframe_deletion': 'In_Frame_Del', + 'missense_variant': 'Missense_Mutation', + 'coding_sequence_variant': 'Missense_Mutation', + 'conservative_missense_variant': 'Missense_Mutation', + 'rare_amino_acid_variant': 'Missense_Mutation', + 'transcript_amplification': 'Intron', + 'intron_variant': 'Intron', + 'INTRAGENIC': 'Intron', + 'intragenic_variant': 'Intron', + 'splice_region_variant': 'Splice_Region', + 'mature_miRNA_variant': 'RNA', + 'exon_variant': 'RNA', + 'non_coding_exon_variant': 'RNA', + 'non_coding_transcript_exon_variant': 'RNA', + 'non_coding_transcript_variant': 'RNA', + 'nc_transcript_variant': 'RNA', + 'stop_retained_variant': 'Silent', + 'synonymous_variant': 'Silent', + 'NMD_transcript_variant': 'Silent', + 'incomplete_terminal_codon_variant': 'Silent', + '5_prime_UTR_variant': "5'UTR", + '5_prime_UTR_premature_start_codon_gain_variant': "5'UTR", + '3_prime_UTR_variant': "3'UTR", + 'intergenic_variant': 'IGR', + 'intergenic_region': 'IGR', + 'regulatory_region_variant': 'IGR', + 'regulatory_region': 'IGR', + 'TF_binding_site_variant': 'IGR', + 'upstream_gene_variant': "5'Flank", + 'downstream_gene_variant': "3'Flank", +} + + +class VariantEffect(): + def __init__(self, variant_type): + self.variant_type = variant_type.capitalize() + assert self.variant_type in ['Snp', 'Ins', 'Del'] + + def __getitem__(self, so_effect): + if so_effect not in so_to_maf or ( + 'frame' in so_effect and self.variant_type == 'Snp' + ): + return 'Targeted_Region' + + ret = so_to_maf[so_effect] + if ret == 'Frame_Shift_': + ret += self.variant_type + return ret + + +infile = sys.argv[1] +if len(sys.argv) > 2: + tumor_sample_name = sys.argv[2] +if len(sys.argv) > 3: + normal_sample_name = sys.argv[3] + +start_pos_idx = None +ref_idx = None +alt_idx = None +variant_type_idx = None +variant_classification_idx = None +gt_alt_depths_idx = {} +gt_ref_depths_idx = {} +gts_idx = {} +samples = set() +required_fields = [ + 'Hugo_Symbol', + 'NCBI_Build', + 'Variant_Type', + 'Variant_Classification', + 'Tumor_Sample_Barcode', + 'HGVSp_Short' +] + + +with open(infile) as data_in: + cols = data_in.readline().rstrip().split('\t') + for field in required_fields: + if field not in cols: + raise IndexError( + 'Cannot generate valid MAF without the following input ' + 'columns: {0}.\n' + 'Missing column: "{1}"' + .format(required_fields, field) + ) + for i, col in enumerate(cols): + if col == 'Variant_Type': + variant_type_idx = i + elif col == 'Variant_Classification': + variant_classification_idx = i + elif col == 'Start_Position': + start_pos_idx = i + elif col == 'Reference_Allele': + ref_idx = i + elif col == 'alt': + alt_idx = i + else: + column, _, sample = col.partition('.') + if sample: + if column == 'gt_alt_depths': + gt_alt_depths_idx[sample] = i + elif column == 'gt_ref_depths': + gt_ref_depths_idx[sample] = i + elif column == 'gts': + gts_idx[sample] = i + else: + # not a recognized sample-specific column + continue + samples.add(sample) + + if ref_idx is None: + raise IndexError('Input file does not have a column "Reference_Allele".') + + if not tumor_sample_name: + if normal_sample_name: + raise ValueError( + 'Normal sample name requires the tumor sample name to be ' + 'specified, too.' + ) + if len(samples) > 1: + raise ValueError( + 'A tumor sample name is required with more than one sample ' + 'in the input.' + ) + if samples: + # There is a single sample with genotype data. + # Assume its the tumor sample. + tumor_sample_name = next(iter(samples)) + else: + if tumor_sample_name not in samples: + raise ValueError( + 'Could not find information about the specified tumor sample ' + 'in the input.' + ) + if tumor_sample_name == normal_sample_name: + raise ValueError( + 'Need different names for the normal and the tumor sample.' + ) + + if normal_sample_name and normal_sample_name not in samples: + raise ValueError( + 'Could not find information about the specified normal sample ' + 'in the input.' + ) + + # All input data checks passed! + # Now extract just the relevant index numbers for the tumor/normal pair + gts_idx = ( + gts_idx.get(tumor_sample_name, alt_idx), + gts_idx.get(normal_sample_name) + ) + gt_alt_depths_idx = ( + gt_alt_depths_idx.get(tumor_sample_name), + gt_alt_depths_idx.get(normal_sample_name) + ) + gt_ref_depths_idx = ( + gt_ref_depths_idx.get(tumor_sample_name), + gt_ref_depths_idx.get(normal_sample_name) + ) + + # Echo all MAF column names + cols_to_print = [] + for n in range(len(cols)): + if n in gts_idx: + continue + if n in gt_alt_depths_idx: + continue + if n in gt_ref_depths_idx: + continue + if n != alt_idx: + cols_to_print.append(n) + + print('\t'.join([cols[n] for n in cols_to_print])) + + for line in data_in: + cols = line.rstrip().split('\t') + + gt_alt_depths = [ + int(cols[ad_idx]) if ad_idx else '' + for ad_idx in gt_alt_depths_idx + ] + gt_ref_depths = [ + int(cols[rd_idx]) if rd_idx else '' + for rd_idx in gt_ref_depths_idx + ] + + gts = [ + ['', ''], + ['', ''] + ] + for n, gt_idx in enumerate(gts_idx): + if gt_idx: + gt_sep = '/' if '/' in cols[gt_idx] else '|' + allele1, _, allele2 = [ + '' if allele == '.' else allele + for allele in cols[gt_idx].partition(gt_sep) + ] + # follow cBioportal recommendation to leave allele1 empty + # when information is not avaliable + if not allele2: + gts[n] = [allele2, allele1] + else: + gts[n] = [allele1, allele2] + if not gts: + gts = [['', ''], ['', '']] + + if cols[variant_type_idx].lower() in ['ins', 'del']: + # transform VCF-style indel representations into MAF ones + ref_allele = cols[ref_idx] + for n, nucs in enumerate( + zip( + ref_allele, + *[allele for gt in gts for allele in gt if allele] + ) + ): + if any(nuc != nucs[0] for nuc in nucs[1:]): + break + else: + n += 1 + if n > 0: + cols[ref_idx] = cols[ref_idx][n:] or '-' + for gt in gts: + for idx, allele in enumerate(gt): + if allele: + gt[idx] = allele[n:] or '-' + if cols[ref_idx] == '-': + n -= 1 + cols[start_pos_idx] = str(int(cols[start_pos_idx]) + n) + + # in-place substitution of so_effect with MAF effect + cols[variant_classification_idx] = VariantEffect( + cols[variant_type_idx] + )[cols[variant_classification_idx]] + ret_line = '\t'.join([cols[n] for n in cols_to_print]) + + field_formatters = { + 'tumor_seq_allele1': gts[0][0], + 'tumor_seq_allele2': gts[0][1], + 'match_norm_seq_allele1': gts[1][0], + 'match_norm_seq_allele2': gts[1][1], + 't_alt_count': gt_alt_depths[0], + 'n_alt_count': gt_alt_depths[1], + 't_ref_count': gt_ref_depths[0], + 'n_ref_count': gt_ref_depths[1], + } + + print( + # use safe_substitute here to avoid key errors with column content + # looking like unknown placeholders + string.Template(ret_line).safe_substitute(field_formatters) + )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gemini_query_as_maf_result.tabular Tue Mar 10 06:20:59 2020 -0400 @@ -0,0 +1,39 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer HGVSp_Short t_alt_count t_ref_count n_alt_count n_ref_count +unknown 37 1 10583 10583 5'Flank snp G A novel test Somatic p.= +unknown 37 1 10611 10611 5'Flank snp C G novel test Somatic p.= +unknown 37 1 13302 13302 RNA snp C T novel test Somatic p.= +unknown 37 1 13327 13327 RNA snp G C novel test Somatic p.= +unknown 37 1 13958 13958 RNA del C - novel test Somatic p.= +unknown 37 1 13980 13980 RNA snp T C novel test Somatic p.= +unknown 37 1 30923 30923 3'Flank snp G T novel test Somatic p.= +unknown 37 1 46402 46402 IGR ins - TGT novel test Somatic p.= +unknown 37 1 47190 47190 IGR ins - A novel test Somatic p.= +unknown 37 1 51476 51476 IGR snp T C novel test Somatic p.= +unknown 37 1 51479 51479 IGR snp T A novel test Somatic p.= +unknown 37 1 51914 51914 IGR snp T G novel test Somatic p.= +unknown 37 1 51935 51935 IGR snp C T novel test Somatic p.= +unknown 37 1 51954 51954 IGR snp G C novel test Somatic p.= +unknown 37 1 52058 52058 IGR snp G C novel test Somatic p.= +unknown 37 1 52144 52144 IGR snp T A novel test Somatic p.= +unknown 37 1 52186 52188 IGR del TAA - novel test Somatic p.= +unknown 37 1 52238 52238 IGR snp T G novel test Somatic p.= +unknown 37 1 53235 53236 IGR del AT - novel test Somatic p.= +unknown 37 1 54353 54353 IGR snp C A novel test Somatic p.= +unknown 37 1 54421 54421 IGR snp A G novel test Somatic p.= +unknown 37 1 54490 54490 IGR snp G A novel test Somatic p.= +unknown 37 1 54676 54676 IGR snp C T novel test Somatic p.= +unknown 37 1 54753 54753 IGR snp T G novel test Somatic p.= +unknown 37 1 55164 55164 IGR snp C A novel test Somatic p.= +unknown 37 1 55249 55249 IGR ins - TATGG novel test Somatic p.= +unknown 37 1 55299 55299 IGR snp C T novel test Somatic p.= +unknown 37 1 55313 55313 IGR snp A T novel test Somatic p.= +unknown 37 1 55326 55326 IGR snp T C novel test Somatic p.= +unknown 37 1 55330 55330 IGR snp G A novel test Somatic p.= +unknown 37 1 55367 55367 IGR snp G A novel test Somatic p.= +unknown 37 1 55388 55388 IGR snp C T novel test Somatic p.= +unknown 37 1 55394 55394 IGR snp T A novel test Somatic p.= +unknown 37 1 55416 55416 IGR snp G A novel test Somatic p.= +unknown 37 1 55427 55427 IGR snp T C novel test Somatic p.= +unknown 37 1 55816 55816 IGR snp G A novel test Somatic p.= +unknown 37 1 55850 55850 IGR snp C G novel test Somatic p.= +unknown 37 1 55852 55852 IGR snp G C novel test Somatic p.=