annotate 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"

#!/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__()