def _parse_qresult(self): # initial qresult value qresult = None hit_rows = [] # state values state_QRES_NEW = 1 state_QRES_HITTAB = 3 state_QRES_CONTENT = 5 state_QRES_END = 7 while True: # one line before the hit table if self.line.startswith('The best scores are:'): qres_state = state_QRES_HITTAB # the end of a query or the file altogether elif self.line.strip() == '>>>///' or not self.line: qres_state = state_QRES_END # the beginning of a new query elif not self.line.startswith('>>>') and '>>>' in self.line: qres_state = state_QRES_NEW # the beginning of the query info and its hits + hsps elif self.line.startswith('>>>') and not \ self.line.strip() == '>>><<<': qres_state = state_QRES_CONTENT # default qres mark else: qres_state = None if qres_state is not None: if qres_state == state_QRES_HITTAB: # parse hit table if flag is set hit_rows = self.__parse_hit_table() elif qres_state == state_QRES_END: yield _set_qresult_hits(qresult, hit_rows) break elif qres_state == state_QRES_NEW: # if qresult is filled, yield it first if qresult is not None: yield _set_qresult_hits(qresult, hit_rows) regx = re.search(_RE_ID_DESC_SEQLEN, self.line) query_id = regx.group(1) seq_len = regx.group(3) desc = regx.group(2) qresult = QueryResult(id=query_id) qresult.seq_len = int(seq_len) # get target from the next line self.line = self.handle.readline() qresult.target = [x for x in self.line.split(' ') if x][1].strip() if desc is not None: qresult.description = desc # set values from preamble for key, value in self._preamble.items(): setattr(qresult, key, value) elif qres_state == state_QRES_CONTENT: assert self.line[3:].startswith(qresult.id), self.line for hit, strand in self._parse_hit(query_id): # HACK: re-set desc, for hsp hit and query description hit.description = hit.description hit.query_description = qresult.description # if hit is not in qresult, append it if hit.id not in qresult: qresult.append(hit) # otherwise, it might be the same hit with a different strand else: # make sure strand is different and then append hsp to # existing hit for hsp in hit.hsps: assert strand != hsp.query_strand qresult[hit.id].append(hsp) self.line = self.handle.readline()
def __iter__(self): 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 alphabet based on program if qresult.program == 'blastn': alphabet = generic_dna elif qresult.program in ['blastp', 'blastx', 'tblastn', 'tblastx']: alphabet = generic_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.alphabet = alphabet # 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