Python Hit.seq_len方法代码示例

# 需要导入模块: from Bio.SearchIO._model import Hit [as 别名]
# 或者: from Bio.SearchIO._model.Hit import seq_len [as 别名]
    def _parse_hit(self, query_id):
        while True:
            self.line = self.handle.readline()
            if self.line.startswith('>>'):
                break

        state = _STATE_NONE
        strand = None
        hsp_list = []
        while True:
            peekline = self.handle.peekline()
            # yield hit if we've reached the start of a new query or
            # the end of the search
            if peekline.strip() in [">>><<<", ">>>///"] or \
                    (not peekline.startswith('>>>') and '>>>' in peekline):
                # append last parsed_hsp['hit']['seq'] line
                if state == _STATE_HIT_BLOCK:
                    parsed_hsp['hit']['seq'] += self.line.strip()
                elif state == _STATE_CONS_BLOCK:
                    hsp.aln_annotation['similarity'] += \
                            self.line.strip('\r\n')
                # process HSP alignment and coordinates
                _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                hit = Hit(hsp_list)
                hit.description = hit_desc
                hit.seq_len = seq_len
                yield hit, strand
                hsp_list = []
                break
            # yield hit and create a new one if we're still in the same query
            elif self.line.startswith('>>'):
                # try yielding,  if we have hsps
                if hsp_list:
                    _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                    hit = Hit(hsp_list)
                    hit.description = hit_desc
                    hit.seq_len = seq_len
                    yield hit, strand
                    hsp_list = []
                # try to get the hit id and desc, and handle cases without descs
                try:
                    hit_id, hit_desc = self.line[2:].strip().split(' ', 1)
                except ValueError:
                    hit_id = self.line[2:].strip().split(' ', 1)[0]
                    hit_desc = ''
                # create the HSP object for Hit
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                # set or reset the state to none
                state = _STATE_NONE
                parsed_hsp = {'query': {}, 'hit': {}}
            # create and append a new HSP if line starts with '>--'
            elif self.line.startswith('>--'):
                # set seq attributes of previous hsp
                _set_hsp_seqs(hsp, parsed_hsp, self._preamble['program'])
                # and create a new one
                frag = HSPFragment(hit_id, query_id)
                hsp = HSP([frag])
                hsp_list.append(hsp)
                # set the state ~ none yet
                state = _STATE_NONE
                parsed_hsp = {'query': {}, 'hit': {}}
            # this is either query or hit data in the HSP, depending on the state
            elif self.line.startswith('>'):
                if state == _STATE_NONE:
                    # make sure it's the correct query
                    assert query_id.startswith(self.line[1:].split(' ')[0]), \
                            "%r vs %r" % (query_id, self.line)
                    state = _STATE_QUERY_BLOCK
                    parsed_hsp['query']['seq'] = ''
                elif state == _STATE_QUERY_BLOCK:
                    # make sure it's the correct hit
                    assert hit_id.startswith(self.line[1:].split(' ')[0])
                    state = _STATE_HIT_BLOCK
                    parsed_hsp['hit']['seq'] = ''
            # check for conservation block
            elif self.line.startswith('; al_cons'):
                state = _STATE_CONS_BLOCK
                hsp.fragment.aln_annotation['similarity'] = ''
            elif self.line.startswith(';'):
                # Fasta outputs do not make a clear distinction between Hit
                # and HSPs, so we check the attribute names to determine
                # whether it belongs to a Hit or HSP
                regx = re.search(_RE_ATTR, self.line.strip())
                name = regx.group(1)
                value = regx.group(2)

                # for values before the '>...' query block
                if state == _STATE_NONE:
                    if name in _HSP_ATTR_MAP:
                        attr_name, caster = _HSP_ATTR_MAP[name]
                        if caster is not str:
                            value = caster(value)
                        if name in ['_ident', '_sim']:
                            value *= 100
                        setattr(hsp, attr_name, value)
                # otherwise, pool the values for processing later
                elif state == _STATE_QUERY_BLOCK:
                    parsed_hsp['query'][name] = value
#.........这里部分代码省略.........

# 需要导入模块: from Bio.SearchIO._model import Hit [as 别名]
# 或者: from Bio.SearchIO._model.Hit import seq_len [as 别名]
    def _parse_qresult(self):
        """Generator function that returns QueryResult objects."""
        # state values, determines what to do for each line
        state_EOF = 0
        state_QRES_NEW = 1
        state_QRES_SAME = 3
        state_HIT_NEW = 2
        state_HIT_SAME = 4
        # initial dummy values
        qres_state = None
        file_state = None
        prev_qid, prev_hid = None, None
        cur, prev = None, None
        hit_list, hsp_list = [], []

        while True:
            # store previous line's parsed values for all lines after the first
            if cur is not None:
                prev = cur
                prev_qid = cur_qid
                prev_hid = cur_hid
            # only parse the result row if it's not EOF
            if self.line:
                cur = self._parse_row()
                cur_qid = cur['qname']
                cur_hid = cur['tname']
            else:
                file_state = state_EOF
                # mock values, since we have nothing to parse
                cur_qid, cur_hid = None, None

            # get the state of hit and qresult
            if prev_qid != cur_qid:
                qres_state = state_QRES_NEW
            else:
                qres_state = state_QRES_SAME
            # new hits are hits with different ids or hits in a new qresult
            if prev_hid != cur_hid or qres_state == state_QRES_NEW:
                hit_state = state_HIT_NEW
            else:
                hit_state = state_HIT_SAME

            if prev is not None:
                # create fragment and HSP and set their attributes
                hsp = _create_hsp(prev_hid, prev_qid, prev)
                hsp_list.append(hsp)

                if hit_state == state_HIT_NEW:
                    # create Hit and set its attributes
                    hit = Hit(hsp_list)
                    hit.seq_len = prev['tsize']
                    hit_list.append(hit)
                    hsp_list = []

                # create qresult and yield if we're at a new qresult or at EOF
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(prev_qid)
                    for hit in hit_list:
                        qresult.absorb(hit)
                    qresult.seq_len = prev['qsize']
                    yield qresult
                    # if we're at EOF, break
                    if file_state == state_EOF:
                        break
                    hit_list = []

            self.line = self.handle.readline()

# 需要导入模块: from Bio.SearchIO._model import Hit [as 别名]
# 或者: from Bio.SearchIO._model.Hit import seq_len [as 别名]
    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)

#.........这里部分代码省略.........