diff jbrowse2/blastxml_to_gapped_gff3.py @ 0:cd5d63cd0eb5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse2/blastxml_to_gapped_gff3.py	Wed Jan 03 01:36:39 2024 +0000
@@ -0,0 +1,268 @@
+#!/usr/bin/env python
+import argparse
+import copy
+import logging
+import re
+import sys
+
+from BCBio import GFF
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(name='blastxml2gff3')
+
+__doc__ = """
+BlastXML files, when transformed to GFF3, do not normally show gaps in the
+blast hits. This tool aims to fill that "gap".
+"""
+
+
+def blastxml2gff3(blastxml, min_gap=3, trim=False, trim_end=False, include_seq=False):
+    from Bio.Blast import NCBIXML
+    from Bio.Seq import Seq
+    from Bio.SeqRecord import SeqRecord
+    from Bio.SeqFeature import SeqFeature, SimpleLocation
+
+    blast_records = NCBIXML.parse(blastxml)
+    for idx_record, record in enumerate(blast_records):
+        # http://www.sequenceontology.org/browser/release_2.4/term/SO:0000343
+        match_type = {  # Currently we can only handle BLASTN, BLASTP
+            'BLASTN': 'nucleotide_match',
+            'BLASTP': 'protein_match',
+        }.get(record.application, 'match')
+
+        recid = record.query
+        if ' ' in recid:
+            recid = recid[0:recid.index(' ')]
+
+        rec = SeqRecord(Seq("ACTG"), id=recid)
+        for idx_hit, hit in enumerate(record.alignments):
+            for idx_hsp, hsp in enumerate(hit.hsps):
+                qualifiers = {
+                    "ID": 'b2g.%s.%s.%s' % (idx_record, idx_hit, idx_hsp),
+                    "source": "blast",
+                    "score": hsp.expect,
+                    "accession": hit.accession,
+                    "hit_id": hit.hit_id,
+                    "length": hit.length,
+                    "hit_titles": hit.title.split(' >'),
+                }
+                if include_seq:
+                    qualifiers.update({
+                        'blast_qseq': hsp.query,
+                        'blast_sseq': hsp.sbjct,
+                        'blast_mseq': hsp.match,
+                    })
+
+                for prop in ('score', 'bits', 'identities', 'positives',
+                             'gaps', 'align_length', 'strand', 'frame',
+                             'query_start', 'query_end', 'sbjct_start',
+                             'sbjct_end'):
+                    qualifiers['blast_' + prop] = getattr(hsp, prop, None)
+
+                desc = hit.title.split(' >')[0]
+                qualifiers['description'] = desc[desc.index(' '):]
+
+                # This required a fair bit of sketching out/match to figure out
+                # the first time.
+                #
+                # the match_start location must account for queries and
+                # subjecst that start at locations other than 1
+                parent_match_start = hsp.query_start - hsp.sbjct_start
+                # The end is the start + hit.length because the match itself
+                # may be longer than the parent feature, so we use the supplied
+                # subject/hit length to calculate the real ending of the target
+                # protein.
+                parent_match_end = hsp.query_start + hit.length + hsp.query.count('-')
+
+                # If we trim the left end, we need to trim without losing information.
+                used_parent_match_start = parent_match_start
+                if trim:
+                    if parent_match_start < 1:
+                        used_parent_match_start = 0
+
+                if trim or trim_end:
+                    if parent_match_end > hsp.query_end:
+                        parent_match_end = hsp.query_end + 1
+
+                # The ``match`` feature will hold one or more ``match_part``s
+                top_feature = SeqFeature(
+                    SimpleLocation(used_parent_match_start, parent_match_end, strand=0),
+                    type=match_type,
+                    qualifiers=qualifiers
+                )
+
+                # Unlike the parent feature, ``match_part``s have sources.
+                part_qualifiers = {
+                    "source": "blast",
+                }
+                top_feature.sub_features = []
+                for idx_part, (start, end, cigar) in \
+                        enumerate(generate_parts(hsp.query, hsp.match,
+                                                 hsp.sbjct,
+                                                 ignore_under=min_gap)):
+                    part_qualifiers['Gap'] = cigar
+                    part_qualifiers['ID'] = qualifiers['ID'] + ('.%s' % idx_part)
+
+                    # Otherwise, we have to account for the subject start's location
+                    match_part_start = parent_match_start + hsp.sbjct_start + start - 1
+
+                    # We used to use hsp.align_length here, but that includes
+                    # gaps in the parent sequence
+                    #
+                    # Furthermore align_length will give calculation errors in weird places
+                    # So we just use (end-start) for simplicity
+                    match_part_end = match_part_start + (end - start)
+
+                    top_feature.sub_features.append(
+                        SeqFeature(
+                            SimpleLocation(match_part_start, match_part_end, strand=1),
+                            type="match_part",
+                            qualifiers=copy.deepcopy(part_qualifiers))
+                    )
+
+                rec.features.append(top_feature)
+        rec.annotations = {}
+        yield rec
+
+
+def __remove_query_gaps(query, match, subject):
+    """remove positions in all three based on gaps in query
+
+    In order to simplify math and calculations...we remove all of the gaps
+    based on gap locations in the query sequence::
+
+        Q:ACTG-ACTGACTG
+        S:ACTGAAC---CTG
+
+    will become::
+
+        Q:ACTGACTGACTG
+        S:ACTGAC---CTG
+
+    which greatly simplifies the process of identifying the correct location
+    for a match_part
+    """
+    prev = 0
+    fq = ''
+    fm = ''
+    fs = ''
+    for position in re.finditer('-', query):
+        fq += query[prev:position.start()]
+        fm += match[prev:position.start()]
+        fs += subject[prev:position.start()]
+        prev = position.start() + 1
+    fq += query[prev:]
+    fm += match[prev:]
+    fs += subject[prev:]
+
+    return (fq, fm, fs)
+
+
+def generate_parts(query, match, subject, ignore_under=3):
+    region_q = []
+    region_m = []
+    region_s = []
+
+    (query, match, subject) = __remove_query_gaps(query, match, subject)
+
+    region_start = -1
+    region_end = -1
+    mismatch_count = 0
+    for i, (q, m, s) in enumerate(zip(query, match, subject)):
+
+        # If we have a match
+        if m != ' ' or m == '+':
+            if region_start == -1:
+                region_start = i
+                # It's a new region, we need to reset or it's pre-seeded with
+                # spaces
+                region_q = []
+                region_m = []
+                region_s = []
+            region_end = i
+            mismatch_count = 0
+        else:
+            mismatch_count += 1
+
+        region_q.append(q)
+        region_m.append(m)
+        region_s.append(s)
+
+        if mismatch_count >= ignore_under and region_start != -1 and region_end != -1:
+            region_q = region_q[0:-ignore_under]
+            region_m = region_m[0:-ignore_under]
+            region_s = region_s[0:-ignore_under]
+            yield region_start, region_end + 1, \
+                cigar_from_string(region_q, region_m, region_s, strict_m=True)
+            region_q = []
+            region_m = []
+            region_s = []
+
+            region_start = -1
+            region_end = -1
+            mismatch_count = 0
+
+    yield region_start, region_end + 1, \
+        cigar_from_string(region_q, region_m, region_s, strict_m=True)
+
+
+def _qms_to_matches(query, match, subject, strict_m=True):
+    matchline = []
+
+    for (q, m, s) in zip(query, match, subject):
+        ret = ''
+
+        if m != ' ' or m == '+':
+            ret = '='
+        elif m == ' ':
+            if q == '-':
+                ret = 'D'
+            elif s == '-':
+                ret = 'I'
+            else:
+                ret = 'X'
+        else:
+            log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject))
+
+        if strict_m:
+            if ret == '=' or ret == 'X':
+                ret = 'M'
+
+        matchline.append(ret)
+    return matchline
+
+
+def _matchline_to_cigar(matchline):
+    cigar_line = []
+    last_char = matchline[0]
+    count = 0
+    for char in matchline:
+        if char == last_char:
+            count += 1
+        else:
+            cigar_line.append("%s%s" % (last_char, count))
+            count = 1
+        last_char = char
+    cigar_line.append("%s%s" % (last_char, count))
+    return ' '.join(cigar_line)
+
+
+def cigar_from_string(query, match, subject, strict_m=True):
+    matchline = _qms_to_matches(query, match, subject, strict_m=strict_m)
+    if len(matchline) > 0:
+        return _matchline_to_cigar(matchline)
+    else:
+        return ""
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
+    parser.add_argument('blastxml', type=argparse.FileType("r"), help='Blast XML Output')
+    parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3)
+    parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature')
+    parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene')
+    parser.add_argument('--include_seq', action='store_true', help='Include sequence')
+    args = parser.parse_args()
+
+    for rec in blastxml2gff3(**vars(args)):
+        if len(rec.features):
+            GFF.write([rec], sys.stdout)