def legacy_annotate_mvf(args): """Main method""" args.qprint("Running LegacyAnnotateMVF") mvf = MultiVariantFile(args.mvf, 'read') args.qprint("Input MVF header processed.") args.qprint("MVF flavor: {}".format(mvf.flavor)) gff, geneids = parse_gff_legacy_annotate( args.gff, mvf.contig_data, gene_pattern=args.gene_pattern) args.qprint("GFF processed.") outmvf = MultiVariantFile(args.out, 'write', overwrite=args.overwrite, flavor=mvf.flavor) outmvf.copy_headers_from(mvf) if args.nongenic_mode is False: outmvf.contig_data = geneids.copy() outmvf.contig_indices = list(range(len(geneids))) outmvf.contig_ids = [geneids[x]['id'] for x in outmvf.contig_indices] outmvf.contig_labels = [geneids[x]['label'] for x in outmvf.contig_indices] outmvf.write_data(outmvf.get_header()) args.qprint("Output MVF established.") entrybuffer = [] nentry = 0 args.qprint("Processing MVF entries.") for contigid, pos, allelesets in mvf.iterentries(decode=False): annotated_pos = None if contigid in gff: for (xgeneid, xstart, xstop) in gff[contigid]: if xstart < pos < xstop: annotated_pos = xgeneid + 0 break if args.nongenic_mode is True and args.unmargin > 0: for xpos in range(pos - args.unmargin, pos + args.unmargin + 1): if xstart < xpos < xstop: annotated_pos = xgeneid + 0 break if annotated_pos is not None and not args.nongenic_mode: entrybuffer.append((annotated_pos, pos, allelesets)) elif args.nongenic_mode and annotated_pos is None: entrybuffer.append((contigid, pos, allelesets)) if args.nongenic_mode or annotated_pos is not None: nentry += 1 if nentry == args.line_buffer: args.qprint("Writing block of entries.") outmvf.write_entries(entrybuffer) entrybuffer = [] nentry = 0 if entrybuffer: outmvf.write_entries(entrybuffer) args.qprint("Writing final block of entries.") entrybuffer = [] nentry = 0 return ''
def translate_mvf(args): """Main method""" args.qprint("Running TranslateMVF") if args.gff: args.qprint("Reading and Indexing MVF.") else: args.qprint("Reading MVF.") mvf = MultiVariantFile(args.mvf, 'read', contigindex=bool(args.gff)) if mvf.flavor != 'dna': raise RuntimeError("MVF must be flavor=dna to translate") if args.gff: args.qprint("Processing MVF Index File.") mvf.read_index_file() args.qprint("GFF processing start.") gff_genes, gene_order = parse_gff_exome(args) args.qprint("GFF processed.") outmvf = MultiVariantFile(args.out, 'write', overwrite=args.overwrite) outmvf.copy_headers_from(mvf) outmvf.contig_data = dict( ( i, dict((y, z) for (y, z) in gff_genes[x].items() if y not in ('cds', ))) for (i, x) in enumerate(gene_order)) outmvf.contig_indices = list(range(len(gene_order))) outmvf.contig_ids = [gff_genes[x]['id'] for x in gene_order] outmvf.contig_labels = [gff_genes[x]['label'] for x in gene_order] outmvf.flavor = args.output_data outmvf.metadata.notes.append(args.command_string) outmvf.write_data(outmvf.get_header()) args.qprint("Output MVF Established.") entrybuffer = [] nentry = 0 pos = None if not args.gff: args.qprint("No GFF used, translating sequences as pre-aligned in " "coding frame.") inputbuffer = [] current_contig = '' for contigid, pos, allelesets in mvf.iterentries(decode=False): if current_contig == '': current_contig = contigid[:] if contigid == current_contig: inputbuffer.append((pos, allelesets)) else: for _, amino_acids, alleles in iter_codons( inputbuffer, mvf): if all([x in '-X' for x in amino_acids]): continue if args.output_data == 'protein': entrybuffer.append( (current_contig, pos, (amino_acids,))) else: entrybuffer.append(( current_contig, pos, ( amino_acids, alleles[0], alleles[1], alleles[2]))) nentry += 1 if nentry == args.line_buffer: outmvf.write_entries(entrybuffer) entrybuffer = [] nentry = 0 inputbuffer = [(pos, allelesets)] current_contig = contigid[:] if inputbuffer: for _, amino_acids, alleles in iter_codons( inputbuffer, outmvf): if all([x in '-X' for x in amino_acids]): continue if args.output_data == 'protein': entrybuffer.append( (current_contig, pos, (amino_acids,))) else: entrybuffer.append(( current_contig, pos, ( amino_acids, alleles[0], alleles[1], alleles[2]))) nentry += 1 if nentry == args.line_buffer: outmvf.write_entries(entrybuffer) entrybuffer = [] nentry = 0 else: running_gene_index = -1 for igene, gene in enumerate(gene_order): xcontiglabel = gff_genes[gene]['contig'] xcontig = mvf.get_contig_indices( labels=gff_genes[gene]['contig']) if xcontig is None: print("Warning: contig {} not found".format( gff_genes[gene]['contig'])) xcontigid = mvf.get_contig_ids(indices=xcontig)[0] min_gene_coord = gff_genes[gene]['cds'][0][0] max_gene_coord = gff_genes[gene]['cds'][-1][1] mvf_entries = {} if not igene % 100: args.qprint("Processing gene {} on {}".format( gene, xcontiglabel)) for contigid, pos, allelesets in mvf.itercontigentries( xcontig, decode=False): if pos < min_gene_coord: continue if pos > max_gene_coord: break mvf_entries[pos] = allelesets[0] reverse_strand = gff_genes[gene]['strand'] == '-' coords = [] running_gene_index += 1 for elem in gff_genes[gene]['cds']: coords.extend(list(range(elem[0], elem[1] + 1))) if reverse_strand: coords = coords[::-1] for codoncoord in range(0, len(coords), 3): alleles = tuple(mvf_entries.get(x, '-') for x in coords[codoncoord:codoncoord + 3]) if len(alleles) < 3: alleles = tuple(list(alleles) + ['-'] * (3 - len(alleles))) if all(len(x) == 1 for x in alleles): if reverse_strand: alleles = tuple( MLIB.complement_bases[x] for x in alleles) decoded_alleles = alleles amino_acids = translate_single_codon(''.join(alleles)) else: if reverse_strand is True: decoded_alleles = tuple(tuple(MLIB.complement_bases[y] for y in mvf.decode(x)) for x in alleles) alleles = tuple(outmvf.encode(''.join(x)) for x in decoded_alleles) else: decoded_alleles = tuple(mvf.decode(x) for x in alleles) amino_acids = tuple(translate_single_codon(''.join(x)) for x in zip(*decoded_alleles)) amino_acids = outmvf.encode(''.join(amino_acids)) if args.output_data == 'protein': entrybuffer.append(( ( xcontigid if args.retain_contigs else running_gene_index ), ( coords[codoncoord] if args.retain_coords else codoncoord ), ( amino_acids, ) )) elif args.output_data == 'codon': entrybuffer.append(( ( xcontigid if args.retain_contigs else running_gene_index ), ( coords[codoncoord] if args.retain_coords else codoncoord ), ( amino_acids, alleles[0], alleles[1], alleles[2] ) )) elif args.output_data == 'dna': for j, elem in enumerate( range(codoncoord, min(codoncoord + 3, len(coords)))): entrybuffer.append(( ( xcontigid if args.retain_contigs else running_gene_index ), ( coords[elem] if args.retain_coords else elem + 1 ), ( alleles[j], ) )) nentry += 1 if nentry >= args.line_buffer: args.qprint("Writing a block of {} entries.".format( args.line_buffer)) outmvf.write_entries(entrybuffer) entrybuffer = [] nentry = 0 if entrybuffer: outmvf.write_entries(entrybuffer) entrybuffer = [] nentry = 0 return ''