Mercurial > repos > galaxyp > map_peptides_to_bed
view map_peptides_to_bed.py @ 3:704ea6303c4c draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
author | galaxyp |
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date | Tue, 07 Apr 2020 11:41:15 -0400 |
parents | db90662d26f9 |
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#!/usr/bin/env python """ # #------------------------------------------------------------------------------ # University of Minnesota # Copyright 2014, Regents of the University of Minnesota #------------------------------------------------------------------------------ # Author: # # James E Johnson # #------------------------------------------------------------------------------ Input: list of protein_accessions, peptide_sequence GFF3 with fasta Output: GFF3 of peptides Filter: Must cross splice boundary """ import optparse import os.path import sys from Bio.Seq import ( reverse_complement, translate ) class BedEntry(object): def __init__(self, line): self.line = line try: fields = line.rstrip('\r\n').split('\t') (chrom, chromStart, chromEnd, name, score, strand, thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts) = fields[0:12] seq = fields[12] if len(fields) > 12 else None self.chrom = chrom self.chromStart = int(chromStart) self.chromEnd = int(chromEnd) self.name = name self.score = int(score) self.strand = strand self.thickStart = int(thickStart) self.thickEnd = int(thickEnd) self.itemRgb = itemRgb self.blockCount = int(blockCount) self.blockSizes = [int(x) for x in blockSizes.split(',')] self.blockStarts = [int(x) for x in blockStarts.split(',')] self.seq = seq except Exception as e: sys.stderr.write("Unable to read Bed entry %s \n" % e) exit(1) def __str__(self): return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s%s' % ( self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, ','.join([str(x) for x in self.blockSizes]), ','.join([str(x) for x in self.blockStarts]), '\t%s' % self.seq if self.seq else '') def get_splice_junctions(self): splice_juncs = [] for i in range(self.blockCount - 1): splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i + 1]) splice_juncs.append(splice_junc) return splice_juncs def get_exon_seqs(self): exons = [] for i in range(self.blockCount): # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1]) exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]]) if self.strand == '-': # reverse complement exons.reverse() for i, s in enumerate(exons): exons[i] = reverse_complement(s) return exons def get_spliced_seq(self): seq = ''.join(self.get_exon_seqs()) return seq def get_translation(self, sequence=None): translation = None seq = sequence if sequence else self.get_spliced_seq() if seq: seqlen = int(len(seq) / 3) * 3 if seqlen >= 3: translation = translate(seq[:seqlen]) return translation def get_translations(self): translations = [] seq = self.get_spliced_seq() if seq: for i in range(3): translation = self.get_translation(sequence=seq[i:]) if translation: translations.append(translation) return translations def get_subrange(self, tstart, tstop): """ (start, end) """ chromStart = self.chromStart chromEnd = self.chromEnd r = range(self.blockCount) if self.strand == '-': r = list(r) r.reverse() bStart = 0 for x in r: bEnd = bStart + self.blockSizes[x] # print >> sys.stderr, "%d chromStart: %d chromEnd: %s bStart: %s bEnd: %d\n" % (x, chromStart, chromEnd, bStart, bEnd) if bStart <= tstart < bEnd: if self.strand == '+': chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart) else: chromEnd = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstart - bStart) if bStart <= tstop < bEnd: if self.strand == '+': chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart) else: chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart) bStart += self.blockSizes[x] return(chromStart, chromEnd) def get_blocks(self, chromStart, chromEnd): """ get the blocks for sub range """ tblockCount = 0 tblockSizes = [] tblockStarts = [] for x in range(self.blockCount): bStart = self.chromStart + self.blockStarts[x] bEnd = bStart + self.blockSizes[x] if bStart > chromEnd: break if bEnd < chromStart: continue cStart = max(chromStart, bStart) tblockStarts.append(cStart - chromStart) tblockSizes.append(min(chromEnd, bEnd) - cStart) tblockCount += 1 sys.stderr.write("tblockCount: %d tblockStarts: %s tblockSizes: %s\n" % (tblockCount, tblockStarts, tblockSizes)) return (tblockCount, tblockSizes, tblockStarts) def get_filterd_translations(self, untrimmed=False, filtering=True, ignore_left_bp=0, ignore_right_bp=0): """ [[start, end, seq, blockCount, blockSizes, blockStarts], [start, end, seq, blockCount, blockSizes, blockStarts], [start, end, seq, blockCount, blockSizes, blockStarts]] filter: ignore translation if stop codon in first exon after ignore_left_bp """ translations = [None, None, None, None, None, None] seq = self.get_spliced_seq() ignore = int((ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3) block_sum = sum(self.blockSizes) exon_sizes = self.blockSizes if self.strand == '-': exon_sizes.reverse() splice_sites = [int(sum(exon_sizes[:x]) / 3) for x in range(1, len(exon_sizes))] sys.stderr.write("splice_sites: %s\n" % splice_sites) junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0] if seq: for i in range(3): translation = self.get_translation(sequence=seq[i:]) if translation: tstart = 0 tstop = len(translation) if not untrimmed: tstart = translation.rfind('*', 0, junc) + 1 stop = translation.find('*', junc) tstop = stop if stop >= 0 else len(translation) if filtering and tstart > ignore: continue trimmed = translation[tstart:tstop] # get genomic locations for start and end offset = (block_sum - i) % 3 sys.stderr.write("tstart: %d tstop: %d offset: %d\n" % (tstart, tstop, offset)) if self.strand == '+': chromStart = self.chromStart + i + (tstart * 3) chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3 else: chromStart = self.chromStart + offset + (len(translation) - tstop) * 3 chromEnd = self.chromEnd - i - (tstart * 3) # get the blocks for this translation tblockCount = 0 tblockSizes = [] tblockStarts = [] for x in range(self.blockCount): bStart = self.chromStart + self.blockStarts[x] bEnd = bStart + self.blockSizes[x] if bStart > chromEnd: break if bEnd < chromStart: continue cStart = max(chromStart, bStart) tblockStarts.append(cStart - chromStart) tblockSizes.append(min(chromEnd, bEnd) - cStart) tblockCount += 1 sys.stderr.write("tblockCount: %d tblockStarts: %s tblockSizes: %s\n" % (tblockCount, tblockStarts, tblockSizes)) translations[i] = [chromStart, chromEnd, trimmed, tblockCount, tblockSizes, tblockStarts] return translations def get_seq_id(self, seqtype='unk:unk', reference='', frame=None): """ # Ensembl fasta ID format >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding """ frame_name = '' chromStart = self.chromStart chromEnd = self.chromEnd strand = 1 if self.strand == '+' else -1 if frame is not None: block_sum = sum(self.blockSizes) offset = (block_sum - frame) % 3 frame_name = '_' + str(frame + 1) if self.strand == '+': chromStart += frame chromEnd -= offset else: chromStart += offset chromEnd -= frame location = "chromosome:%s:%s:%s:%s:%s" % (reference, self.chrom, chromStart, chromEnd, strand) seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location) return seq_id def get_line(self, start_offset=0, end_offset=0): if start_offset or end_offset: s_offset = start_offset if start_offset else 0 e_offset = end_offset if end_offset else 0 if s_offset > self.chromStart: s_offset = self.chromStart chrStart = self.chromStart - s_offset chrEnd = self.chromEnd + e_offset blkSizes = self.blockSizes blkSizes[0] += s_offset blkSizes[-1] += e_offset blkStarts = self.blockStarts for i in range(1, self.blockCount): blkStarts[i] += s_offset items = [str(x) for x in [self.chrom, chrStart, chrEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, ','.join([str(x) for x in blkSizes]), ','.join([str(x) for x in blkStarts])]] return '\t'.join(items) + '\n' return self.line def __main__(): # Parse Command Line parser = optparse.OptionParser() parser.add_option('-t', '--translated_bed', dest='translated_bed', default=None, help='A bed file with added 13th column having a translation') parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column') parser.add_option('-p', '--peptide_column', type='int', dest='peptide_column', default=1, help='column ordinal with peptide sequence') parser.add_option('-n', '--name_column', type='int', dest='name_column', default=2, help='column ordinal with protein name') parser.add_option('-s', '--start_column', type='int', dest='start_column', default=None, help='column with peptide start position in protein') parser.add_option('-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation') # parser.add_option('-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file') # parser.add_option('-f', '--fasta', dest='fasta', default=None, help='Protein fasta') parser.add_option('-T', '--gffTags', dest='gffTags', action='store_true', default=False, help='Add #gffTags to bed output for IGV') parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr') (options, args) = parser.parse_args() # Input files if options.input is not None: try: inputPath = os.path.abspath(options.input) inputFile = open(inputPath, 'r') except Exception as e: sys.stderr("failed: %s\n" % e) exit(2) else: inputFile = sys.stdin inputBed = None if options.translated_bed is not None: inputBed = open(os.path.abspath(options.translated_bed), 'r') peptide_column = options.peptide_column - 1 name_column = options.name_column - 1 if options.name_column else None start_column = options.start_column - 1 if options.start_column else None # Read in peptides # peps[prot_name] = [seq] prot_peps = dict() unassigned_peps = set() try: for i, line in enumerate(inputFile): # print >> sys.stderr, "%3d\t%s\n" % (i, line) if line.startswith('#'): continue fields = line.rstrip('\r\n').split('\t') # print >> sys.stderr, "%3d\t%s\n" % (i, fields) if peptide_column < len(fields): peptide = fields[peptide_column] prot_name = fields[name_column] if name_column is not None and name_column < len(fields) else None if prot_name: offset = fields[start_column] if start_column is not None and start_column < len(fields) else -1 if prot_name not in prot_peps: prot_peps[prot_name] = dict() prot_peps[prot_name][peptide] = offset else: unassigned_peps.add(peptide) if options.debug: sys.stderr.write("prot_peps: %s\n" % prot_peps) sys.stderr.write("unassigned_peps: %s\n" % unassigned_peps) except Exception as e: sys.stderr.write("failed: Error reading %s - %s\n" % (options.input if options.input else 'stdin', e)) exit(1) # Output files bed_fh = None if options.bed: bed_fh = open(options.bed, 'w') bed_fh.write('track name="%s" type=bedDetail description="%s" \n' % ('novel_junction_peptides', 'test')) if options.gffTags: bed_fh.write('#gffTags\n') # if options.gff: # gff_fh = open(options.gff, 'w') # gff_fh.write("##gff-version 3.2.1\n") # if options.reference: # gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference)) try: for i, line in enumerate(inputBed): # print >> sys.stderr, "%3d:\t%s\n" % (i, line) if line.startswith('track'): continue entry = BedEntry(line) if entry.name in prot_peps: for (peptide, offset) in prot_peps[entry.name].items(): if offset < 0: offset = entry.seq.find(peptide) if options.debug: sys.stderr.write("%s\t%s\t%d\t%s\n" % (entry.name, peptide, offset, entry.seq)) if offset >= 0: tstart = offset * 3 tstop = tstart + len(peptide) * 3 if options.debug: sys.stderr.write("%d\t%d\t%d\n" % (offset, tstart, tstop)) (pepStart, pepEnd) = entry.get_subrange(tstart, tstop) if options.debug: sys.stderr.write("%d\t%d\t%d\n" % (offset, pepStart, pepEnd)) if bed_fh: entry.thickStart = pepStart entry.thickEnd = pepEnd bedfields = str(entry).split('\t') if options.gffTags: bedfields[3] = "ID=%s;Name=%s" % (entry.name, peptide) bed_fh.write("%s\t%s\t%s\n" % ('\t'.join(bedfields[:12]), peptide, entry.seq)) except Exception as e: sys.stderr.write("failed: Error reading %s - %s\n" % (options.input if options.input else 'stdin', e)) raise if __name__ == "__main__": __main__()