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()
def _parse_hit(self, query_id):
"""Parse hit on query identifier (PRIVATE)."""
while True:
self.line = self.handle.readline()
if self.line.startswith(">>"):
break
state = _STATE_NONE
strand = None
hsp_list = []
hsp = None
parsed_hsp = None
hit_desc = None
seq_len = None
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
if not query_id.startswith(self.line[1:].split(" ")[0]):
raise ValueError("%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
elif state == _STATE_HIT_BLOCK:
if name == "_len":
seq_len = int(value)
else:
parsed_hsp["hit"][name] = value
# for values in the hit block
else:
raise ValueError("Unexpected line: %r" % self.line)
# otherwise, it must be lines containing the sequences
else:
assert ">" not in self.line
# if we're in hit, parse into hsp.hit
if state == _STATE_HIT_BLOCK:
parsed_hsp["hit"]["seq"] += self.line.strip()
elif state == _STATE_QUERY_BLOCK:
parsed_hsp["query"]["seq"] += self.line.strip()
elif state == _STATE_CONS_BLOCK:
hsp.fragment.aln_annotation["similarity"] += \
self.line.strip("\r\n")
# we should not get here!
else:
raise ValueError("Unexpected line: %r" % self.line)
self.line = self.handle.readline()
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
elif state == _STATE_HIT_BLOCK:
if name == '_len':
seq_len = int(value)
else:
parsed_hsp['hit'][name] = value
# for values in the hit block
else:
raise ValueError("Unexpected line: %r" % self.line)
# otherwise, it must be lines containing the sequences
else:
assert '>' not in self.line
# if we're in hit, parse into hsp.hit
if state == _STATE_HIT_BLOCK:
parsed_hsp['hit']['seq'] += self.line.strip()
elif state == _STATE_QUERY_BLOCK:
parsed_hsp['query']['seq'] += self.line.strip()
elif state == _STATE_CONS_BLOCK:
hsp.fragment.aln_annotation['similarity'] += \
self.line.strip('\r\n')
# we should not get here!
else:
raise ValueError("Unexpected line: %r" % self.line)
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
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
def _parse_qresult(self):
"""Yield QueryResult objects (PRIVATE)."""
# 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
cur_qid, cur_hid = None, 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(id=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()
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
