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 _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 _parse_qresult(self):
"""Parses query results."""
# parse the queries
for event, qresult_elem in self.xml_iter:
# </Iteration> marks the end of a single query
# which means we can process it
if event == 'end' and qresult_elem.tag == 'Iteration':
# we'll use the following schema
# <!ELEMENT Iteration (
# Iteration_iter-num,
# Iteration_query-ID?,
# Iteration_query-def?,
# Iteration_query-len?,
# Iteration_hits?,
# Iteration_stat?,
# Iteration_message?)>
# assign query attributes with fallbacks
query_id = qresult_elem.findtext('Iteration_query-ID')
if query_id is None:
query_id = self._fallback['id']
query_desc = qresult_elem.findtext('Iteration_query-def')
if query_desc is None:
query_desc = self._fallback['description']
query_len = qresult_elem.findtext('Iteration_query-len')
if query_len is None:
query_len = self._fallback['len']
# handle blast searches against databases with Blast's IDs
# 'Query_' marks the beginning of a BLAST+-generated ID,
# 'lcl|' marks the beginning of a BLAST legacy-generated ID
if query_id.startswith('Query_') or query_id.startswith('lcl|'):
# store the Blast-generated query ID
blast_query_id = query_id
id_desc = query_desc.split(' ', 1)
query_id = id_desc[0]
try:
query_desc = id_desc[1]
except IndexError:
query_desc = ''
else:
blast_query_id = ''
hit_list, key_list = [], []
for hit in self._parse_hit(qresult_elem.find('Iteration_hits'),
query_id):
if hit:
# need to keep track of hit IDs, since there could be duplicates,
if hit.id in key_list:
warnings.warn("Adding hit with BLAST-generated ID "
"%r since hit ID %r is already present "
"in query %r. Your BLAST database may contain "
"duplicate entries." %
(hit._blast_id, hit.id, query_id), BiopythonParserWarning)
# fallback to Blast-generated IDs, if the ID is already present
# and restore the desc, too
hit.description = '%s %s' % (hit.id, hit.description)
hit.id = hit._blast_id
# and change the hit_id of the HSPs contained
for hsp in hit:
hsp.hit_id = hit._blast_id
else:
key_list.append(hit.id)
hit_list.append(hit)
# create qresult and assign its attributes
qresult = QueryResult(hit_list, query_id)
qresult.description = query_desc
qresult.seq_len = int(query_len)
qresult._blast_id = blast_query_id
for key, value in self._meta.items():
setattr(qresult, key, value)
# statistics are stored in Iteration_stat's 'grandchildren' with the
# following DTD
# <!ELEMENT Statistics (
# Statistics_db-num,
# Statistics_db-len,
# Statistics_hsp-len,
# Statistics_eff-space,
# Statistics_kappa,
# Statistics_lambda,
# Statistics_entropy)>
stat_iter_elem = qresult_elem.find('Iteration_stat')
if stat_iter_elem is not None:
stat_elem = stat_iter_elem.find('Statistics')
for key, val_info in _ELEM_QRESULT_OPT.items():
value = stat_elem.findtext(key)
if value is not None:
caster = val_info[1]
# recast only if value is not intended to be str
if value is not None and caster is not str:
value = caster(value)
setattr(qresult, val_info[0], value)
# delete element after we finish parsing it
qresult_elem.clear()
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):
"""Parses query results."""
# parse the queries
for event, qresult_elem in self.xml_iter:
# </Iteration> marks the end of a single query
# which means we can process it
if event == 'end' and qresult_elem.tag == 'Iteration':
# we'll use the following schema
# <!ELEMENT Iteration (
# Iteration_iter-num,
# Iteration_query-ID?,
# Iteration_query-def?,
# Iteration_query-len?,
# Iteration_hits?,
# Iteration_stat?,
# Iteration_message?)>
# assign query attributes with fallbacks
query_id = qresult_elem.findtext('Iteration_query-ID')
if query_id is None:
query_id = self._fallback['id']
query_desc = qresult_elem.findtext('Iteration_query-def')
if query_desc is None:
query_desc = self._fallback['description']
query_len = qresult_elem.findtext('Iteration_query-len')
if query_len is None:
query_len = self._fallback['len']
# handle blast searches against databases with Blast's IDs
# 'Query_' marks the beginning of a BLAST+-generated ID,
# 'lcl|' marks the beginning of a BLAST legacy-generated ID
if query_id.startswith('Query_') or query_id.startswith(
'lcl|'):
# store the Blast-generated query ID
blast_query_id = query_id
id_desc = query_desc.split(' ', 1)
query_id = id_desc[0]
try:
query_desc = id_desc[1]
except IndexError:
query_desc = ''
else:
blast_query_id = ''
hit_list, key_list = [], []
for hit in self._parse_hit(qresult_elem.find('Iteration_hits'),
query_id):
if hit:
# need to keep track of hit IDs, since there could be duplicates,
if hit.id in key_list:
warnings.warn(
"Adding hit with BLAST-generated ID "
"%r since hit ID %r is already present "
"in query %r. Your BLAST database may contain "
"duplicate entries." %
(hit._blast_id, hit.id, query_id),
BiopythonParserWarning)
# fallback to Blast-generated IDs, if the ID is already present
# and restore the desc, too
hit.description = '%s %s' % (hit.id,
hit.description)
hit.id = hit._blast_id
# and change the hit_id of the HSPs contained
for hsp in hit:
hsp.hit_id = hit._blast_id
else:
key_list.append(hit.id)
hit_list.append(hit)
# create qresult and assign its attributes
qresult = QueryResult(hit_list, query_id)
qresult.description = query_desc
qresult.seq_len = int(query_len)
qresult._blast_id = blast_query_id
for key, value in self._meta.items():
setattr(qresult, key, value)
# statistics are stored in Iteration_stat's 'grandchildren' with the
# following DTD
# <!ELEMENT Statistics (
# Statistics_db-num,
# Statistics_db-len,
# Statistics_hsp-len,
# Statistics_eff-space,
# Statistics_kappa,
# Statistics_lambda,
# Statistics_entropy)>
stat_iter_elem = qresult_elem.find('Iteration_stat')
if stat_iter_elem is not None:
stat_elem = stat_iter_elem.find('Statistics')
for key, val_info in _ELEM_QRESULT_OPT.items():
value = stat_elem.findtext(key)
if value is not None:
caster = val_info[1]
# recast only if value is not intended to be str
if value is not None and caster is not str:
value = caster(value)
setattr(qresult, val_info[0], value)
# delete element after we finish parsing it
qresult_elem.clear()
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
