def parse_qresult(self):
"""Parse a HMMER2 query block."""
while self.read_next():
if not self.line.startswith('Query'):
raise StopIteration()
_, id_ = self.parse_key_value()
self.qresult = QueryResult(id=id_)
description = None
while self.read_next() and not self.line.startswith('Scores'):
if self.line.startswith('Accession'):
self.qresult.accession = self.parse_key_value()[1]
if self.line.startswith('Description'):
description = self.parse_key_value()[1]
hit_placeholders = self.parse_hits()
if len(hit_placeholders) > 0:
self.parse_hsps(hit_placeholders)
self.parse_hsp_alignments()
while not self.line.startswith('Query'):
self.read_next()
if not self.line:
break
self.buf.append(self.line)
if description is not None:
self.qresult.description = description
yield self.qresult
def _parse_qresult(self):
"""Parses a HMMER3 query block."""
self._read_until(lambda line: line.startswith('Query:'))
while self.line:
# get query id and length
regx = re.search(_QRE_ID_LEN, self.line)
qid = regx.group(1).strip()
# store qresult attributes
qresult_attrs = {
'seq_len': int(regx.group(2)),
'program': self._meta.get('program'),
'version': self._meta.get('version'),
'target': self._meta.get('target'),
}
# get description and accession, if they exist
qdesc = '<unknown description>' # placeholder
while not self.line.startswith('Scores for '):
self.line = read_forward(self.handle)
if self.line.startswith('Accession:'):
acc = self.line.strip().split(' ', 1)[1]
qresult_attrs['accession'] = acc.strip()
elif self.line.startswith('Description:'):
qdesc = self.line.strip().split(' ', 1)[1].strip()
qresult_attrs['description'] = qdesc
# parse the query hits
while self.line and '//' not in self.line:
hit_list = self._parse_hit(qid, qdesc)
# read through the statistics summary
# TODO: parse and store this information?
if self.line.startswith('Internal pipeline'):
while self.line and '//' not in self.line:
self.line = read_forward(self.handle)
# create qresult, set its attributes and yield
# not initializing hit_list directly to handle empty hits
# (i.e. need to set its query description manually)
qresult = QueryResult(id=qid, hits=hit_list)
for attr, value in qresult_attrs.items():
setattr(qresult, attr, value)
yield qresult
self.line = read_forward(self.handle)
# HMMER >= 3.1 outputs '[ok]' at the end of all results file,
# which means we can break the main loop when we see the line
if '[ok]' in self.line:
break
def _parse_commented_qresult(self):
"""Iterator returning `QueryResult` objects from a commented file."""
while True:
comments = self._parse_comments()
if comments:
try:
self.fields = comments['fields']
# iterator for the query results
qres_iter = self._parse_qresult()
except KeyError:
# no fields means the query has no results
assert 'fields' not in comments
# create an iterator returning one empty qresult
# if the query has no results
qres_iter = iter([QueryResult()])
for qresult in qres_iter:
for key, value in comments.items():
setattr(qresult, key, value)
yield qresult
else:
break
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):
"""Generator function that returns QueryResult objects."""
# state values, used to determine what to do with each line
state_EOF = 0
state_QRES_NEW = 1
state_QRES_SAME = 3
state_HIT_NEW = 2
state_HIT_SAME = 4
# dummies for initial states
qres_state = None
hit_state = None
file_state = None
# dummies for initial id caches
prev_qid = None
prev_hid = None
# dummies for initial parsed value containers
cur, prev = None, None
hit_list, hsp_list = [], []
while True:
# store previous line's parsed values if we've past the first line
if cur is not None:
prev = cur
prev_qid = cur_qid
prev_hid = cur_hid
# only parse the line if it's not EOF or not a comment line
if self.line and not self.line.startswith('#'):
cur = self._parse_result_row()
cur_qid = self._get_id(cur['qresult'])
cur_hid = self._get_id(cur['hit'])
else:
file_state = state_EOF
# mock values for cur_qid and cur_hid since the line is empty
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 id 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
# we're creating objects for the previously parsed line(s),
# so nothing is done in the first parsed line (prev == None)
if prev is not None:
# every line is essentially an HSP with one fragment, so we
# create both of these for every line
frag = HSPFragment(prev_hid, prev_qid)
for attr, value in prev['frag'].items():
# adjust coordinates to Python range
# NOTE: this requires both start and end coords to be
# present, otherwise a KeyError will be raised.
# Without this limitation, we might misleadingly set the
# start / end coords
for seq_type in ('query', 'hit'):
if attr == seq_type + '_start':
value = min(value,
prev['frag'][seq_type + '_end']) - 1
elif attr == seq_type + '_end':
value = max(value,
prev['frag'][seq_type + '_start'])
setattr(frag, attr, value)
# strand and frame setattr require the full parsed values
# to be set first
for seq_type in ('hit', 'query'):
# try to set hit and query frame
frame = self._get_frag_frame(frag, seq_type, prev['frag'])
setattr(frag, '%s_frame' % seq_type, frame)
# try to set hit and query strand
strand = self._get_frag_strand(frag, seq_type,
prev['frag'])
setattr(frag, '%s_strand' % seq_type, strand)
hsp = HSP([frag])
for attr, value in prev['hsp'].items():
setattr(hsp, attr, value)
hsp_list.append(hsp)
# create hit and append to temp hit container if hit_state
# says we're not at the same hit or at a new query
if hit_state == state_HIT_NEW:
hit = Hit(hsp_list)
for attr, value in prev['hit'].items():
setattr(hit, attr, value)
hit_list.append(hit)
hsp_list = []
# create qresult and yield if we're at a new qresult or EOF
if qres_state == state_QRES_NEW or file_state == state_EOF:
qresult = QueryResult(hit_list, prev_qid)
for attr, value in prev['qresult'].items():
setattr(qresult, attr, value)
yield qresult
# if current line is EOF, break
if file_state == state_EOF:
break
hit_list = []
self.line = self.handle.readline().strip()
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
# initial value dummies
qres_state = None
file_state = None
prev_qid = None
cur, prev = None, None
# container for Hit objects, used to create QueryResult
hit_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
# only parse the result row if it's not EOF
# NOTE: we are not parsing the extra '#' lines appended to the end
# of hmmer31b1 tabular results since storing them in qresult
# objects means we can not do a single-pass parsing
if self.line and not self.line.startswith('#'):
cur = self._parse_row()
cur_qid = cur['qresult']['id']
else:
file_state = state_EOF
# mock value for cur_qid, since we have nothing to parse
cur_qid = None
if prev_qid != cur_qid:
qres_state = state_QRES_NEW
else:
qres_state = state_QRES_SAME
if prev is not None:
# since domain tab formats only have 1 Hit per line
# we always create HSPFragment, HSP, and Hit per line
prev_hid = prev['hit']['id']
# create fragment and HSP and set their attributes
frag = HSPFragment(prev_hid, prev_qid)
for attr, value in prev['frag'].items():
setattr(frag, attr, value)
hsp = HSP([frag])
for attr, value in prev['hsp'].items():
setattr(hsp, attr, value)
# create Hit and set its attributes
hit = Hit([hsp])
for attr, value in prev['hit'].items():
setattr(hit, attr, value)
hit_list.append(hit)
# 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(hit_list, prev_qid)
for attr, value in prev['qresult'].items():
setattr(qresult, attr, value)
yield qresult
# if we're at EOF, break
if file_state == state_EOF:
break
hit_list = []
self.line = self.handle.readline()
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(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 _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 _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
# dummies for initial states
qres_state = None
hit_state = None
file_state = None
# dummies for initial id caches
prev_qid = None
prev_hid = None
# dummies for initial parsed value containers
cur, prev = None, None
hit_list, hsp_list = [], []
while True:
# store previous line's parsed values, for every line after the 1st
if cur is not None:
prev = cur
prev_qid = cur_qid
prev_hid = cur_hid
# only parse the line if it's not EOF
if self.line and not self.line.startswith('#'):
cur = self._parse_row()
cur_qid = cur['qresult']['id']
cur_hid = cur['hit']['id']
else:
file_state = state_EOF
# mock ID values since the line is empty
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
# start creating objects after the first line (i.e. prev is filled)
if prev is not None:
# each line is basically an HSP with one HSPFragment
frag = HSPFragment(prev_hid, prev_qid)
for attr, value in prev['frag'].items():
setattr(frag, attr, value)
hsp = HSP([frag])
for attr, value in prev['hsp'].items():
setattr(hsp, attr, value)
hsp_list.append(hsp)
# create hit object when we've finished parsing all its hsps
# i.e. when hit state is state_HIT_NEW
if hit_state == state_HIT_NEW:
hit = Hit(hsp_list)
for attr, value in prev['hit'].items():
setattr(hit, attr, value)
hit_list.append(hit)
hsp_list = []
# create qresult and yield if we're at a new qresult or EOF
if qres_state == state_QRES_NEW or file_state == state_EOF:
qresult = QueryResult(hit_list, prev_qid)
for attr, value in prev['qresult'].items():
setattr(qresult, attr, value)
yield qresult
# if current line is EOF, break
if file_state == state_EOF:
break
hit_list = []
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 _parse_qresult(self):
# state values
state_EOF = 0
state_QRES_NEW = 1
state_QRES_SAME = 3
state_HIT_NEW = 2
state_HIT_SAME = 4
# initial dummies
qres_state, hit_state = None, None
file_state = None
prev_qid, prev_hid = None, None
cur, prev = None, None
hit_list, hsp_list = [], []
# if the file has c4 alignments, use that as the alignment mark
if self.has_c4_alignment:
self._ALN_MARK = 'C4 Alignment:'
while True:
self.read_until(lambda line: line.startswith(self._ALN_MARK))
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:
assert self.line.startswith(self._ALN_MARK), self.line
# create temp dicts for storing parsed values
header = {'qresult': {}, 'hit': {}, 'hsp': {}}
# if the file has c4 alignments, try to parse the header
if self.has_c4_alignment:
self.read_until(
lambda line: line.strip().startswith('Query:'))
header = self._parse_alignment_header()
# parse the block contents
cur = self.parse_alignment_block(header)
cur_qid = cur['qresult']['id']
cur_hid = cur['hit']['id']
elif not self.line or self.line.startswith('-- completed '):
file_state = state_EOF
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 query
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:
hsp = _create_hsp(prev_hid, prev_qid, prev['hsp'])
hsp_list.append(hsp)
if hit_state == state_HIT_NEW:
hit = Hit(hsp_list)
for attr, value in prev['hit'].items():
setattr(hit, attr, value)
hit_list.append(hit)
hsp_list = []
if qres_state == state_QRES_NEW or file_state == state_EOF:
qresult = QueryResult(id=prev_qid)
for hit in hit_list:
# not using append since Exonerate may separate the
# same hit if it has different strands
qresult.absorb(hit)
for attr, value in prev['qresult'].items():
setattr(qresult, attr, value)
yield qresult
if file_state == state_EOF:
break
hit_list = []
# only readline() here if we're not parsing C4 alignments
# C4 alignments readline() is handled by its parse_alignment_block
# function
if not self.has_c4_alignment:
self.line = self.handle.readline()
