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| # Copyright 2012 by Wibowo Arindrarto. All rights reserved. | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Bio.SearchIO parser for BLAST+ plain text output formats. | |
| At the moment this is a wrapper around Biopython's NCBIStandalone text | |
| parser (which is now deprecated). | |
| """ | |
| from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment | |
| from Bio.SearchIO._legacy import NCBIStandalone | |
| __all__ = ("BlastTextParser",) | |
| class BlastTextParser: | |
| """Parser for the BLAST text format.""" | |
| def __init__(self, handle): | |
| """Initialize the class.""" | |
| self.handle = handle | |
| blast_parser = NCBIStandalone.BlastParser() | |
| self.blast_iter = NCBIStandalone.Iterator(handle, blast_parser) | |
| def __iter__(self): | |
| """Iterate over BlastTextParser, yields query results.""" | |
| for rec in self.blast_iter: | |
| # set attributes to SearchIO's | |
| # get id and desc | |
| if rec.query.startswith(">"): | |
| rec.query = rec.query[1:] | |
| try: | |
| qid, qdesc = rec.query.split(" ", 1) | |
| except ValueError: | |
| qid, qdesc = rec.query, "" | |
| qdesc = qdesc.replace("\n", "").replace("\r", "") | |
| qresult = QueryResult(id=qid) | |
| qresult.program = rec.application.lower() | |
| qresult.target = rec.database | |
| qresult.seq_len = rec.query_letters | |
| qresult.version = rec.version | |
| # determine molecule_type based on program | |
| if qresult.program == "blastn": | |
| molecule_type = "DNA" | |
| elif qresult.program in ["blastp", "blastx", "tblastn", "tblastx"]: | |
| molecule_type = "protein" | |
| # iterate over the 'alignments' (hits) and the hit table | |
| for idx, aln in enumerate(rec.alignments): | |
| # get id and desc | |
| if aln.title.startswith("> "): | |
| aln.title = aln.title[2:] | |
| elif aln.title.startswith(">"): | |
| aln.title = aln.title[1:] | |
| try: | |
| hid, hdesc = aln.title.split(" ", 1) | |
| except ValueError: | |
| hid, hdesc = aln.title, "" | |
| hdesc = hdesc.replace("\n", "").replace("\r", "") | |
| # iterate over the hsps and group them in a list | |
| hsp_list = [] | |
| for bhsp in aln.hsps: | |
| frag = HSPFragment(hid, qid) | |
| frag.molecule_type = molecule_type | |
| # set alignment length | |
| frag.aln_span = bhsp.identities[1] | |
| # set frames | |
| try: | |
| frag.query_frame = int(bhsp.frame[0]) | |
| except IndexError: | |
| if qresult.program in ("blastp", "tblastn"): | |
| frag.query_frame = 0 | |
| else: | |
| frag.query_frame = 1 | |
| try: | |
| frag.hit_frame = int(bhsp.frame[1]) | |
| except IndexError: | |
| if qresult.program in ("blastp", "tblastn"): | |
| frag.hit_frame = 0 | |
| else: | |
| frag.hit_frame = 1 | |
| # set query coordinates | |
| frag.query_start = min(bhsp.query_start, bhsp.query_end) - 1 | |
| frag.query_end = max(bhsp.query_start, bhsp.query_end) | |
| # set hit coordinates | |
| frag.hit_start = min(bhsp.sbjct_start, bhsp.sbjct_end) - 1 | |
| frag.hit_end = max(bhsp.sbjct_start, bhsp.sbjct_end) | |
| # set query, hit sequences and its annotation | |
| qseq = "" | |
| hseq = "" | |
| midline = "" | |
| for seqtrio in zip(bhsp.query, bhsp.sbjct, bhsp.match): | |
| qchar, hchar, mchar = seqtrio | |
| if qchar == " " or hchar == " ": | |
| assert all(" " == x for x in seqtrio) | |
| else: | |
| qseq += qchar | |
| hseq += hchar | |
| midline += mchar | |
| frag.query, frag.hit = qseq, hseq | |
| frag.aln_annotation["similarity"] = midline | |
| # create HSP object with the fragment | |
| hsp = HSP([frag]) | |
| hsp.evalue = bhsp.expect | |
| hsp.bitscore = bhsp.bits | |
| hsp.bitscore_raw = bhsp.score | |
| # set gap | |
| try: | |
| hsp.gap_num = bhsp.gaps[0] | |
| except IndexError: | |
| hsp.gap_num = 0 | |
| # set identity | |
| hsp.ident_num = bhsp.identities[0] | |
| hsp.pos_num = bhsp.positives[0] | |
| if hsp.pos_num is None: | |
| hsp.pos_num = hsp[0].aln_span | |
| hsp_list.append(hsp) | |
| hit = Hit(hsp_list) | |
| hit.seq_len = aln.length | |
| hit.description = hdesc | |
| qresult.append(hit) | |
| qresult.description = qdesc | |
| yield qresult | |
| # if not used as a module, run the doctest | |
| if __name__ == "__main__": | |
| from Bio._utils import run_doctest | |
| run_doctest() | |