def _create_hsp(hid, qid, hspd):
"""Returns a list of HSP objects from the given parsed HSP values."""
frags = []
# we are iterating over query_ranges, but hit_ranges works just as well
for idx, qcoords in enumerate(hspd['query_ranges']):
# get sequences, create object
hseqlist = hspd.get('hit')
hseq = '' if hseqlist is None else hseqlist[idx]
qseqlist = hspd.get('query')
qseq = '' if qseqlist is None else qseqlist[idx]
frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
# coordinates
frag.query_start = qcoords[0]
frag.query_end = qcoords[1]
frag.hit_start = hspd['hit_ranges'][idx][0]
frag.hit_end = hspd['hit_ranges'][idx][1]
# alignment annotation
try:
aln_annot = hspd.get('aln_annotation', {})
for key, value in aln_annot.items():
frag.aln_annotation[key] = value[idx]
except IndexError:
pass
# strands
frag.query_strand = hspd['query_strand']
frag.hit_strand = hspd['hit_strand']
# and append the hsp object to the list
if frag.aln_annotation.get('similarity') is not None:
if '#' in frag.aln_annotation['similarity']:
frags.extend(_split_fragment(frag))
continue
# try to set frame if there are translation in the alignment
if len(frag.aln_annotation) > 1 or \
frag.query_strand == 0 or \
('vulgar_comp' in hspd and re.search(_RE_TRANS, hspd['vulgar_comp'])):
_set_frame(frag)
frags.append(frag)
# if the query is protein, we need to change the hit and query sequences
# from three-letter amino acid codes to one letter, and adjust their
# coordinates accordingly
if len(frags[0].aln_annotation) == 2: # 2 annotations == protein query
frags = _adjust_aa_seq(frags)
hsp = HSP(frags)
# set hsp-specific attributes
for attr in ('score', 'hit_split_codons', 'query_split_codons', 'model',
'vulgar_comp', 'cigar_comp', 'alphabet'):
if attr in hspd:
setattr(hsp, attr, hspd[attr])
return hsp
def _create_hsp(hid, qid, hspd):
"""Returns a list of HSP objects from the given parsed HSP values."""
frags = []
# we are iterating over query_ranges, but hit_ranges works just as well
for idx, qcoords in enumerate(hspd['query_ranges']):
# get sequences, create object
hseqlist = hspd.get('hit')
hseq = '' if hseqlist is None else hseqlist[idx]
qseqlist = hspd.get('query')
qseq = '' if qseqlist is None else qseqlist[idx]
frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
# coordinates
frag.query_start = qcoords[0]
frag.query_end = qcoords[1]
frag.hit_start = hspd['hit_ranges'][idx][0]
frag.hit_end = hspd['hit_ranges'][idx][1]
# alignment annotation
try:
aln_annot = hspd.get('aln_annotation', {})
for key, value in aln_annot.items():
frag.aln_annotation[key] = value[idx]
except IndexError:
pass
# strands
frag.query_strand = hspd['query_strand']
frag.hit_strand = hspd['hit_strand']
# and append the hsp object to the list
if frag.aln_annotation.get('similarity') is not None:
if '#' in frag.aln_annotation['similarity']:
frags.extend(_split_fragment(frag))
continue
# try to set frame if there are translation in the alignment
if len(frag.aln_annotation) > 1 or \
frag.query_strand == 0 or \
('vulgar_comp' in hspd and re.search(_RE_TRANS, hspd['vulgar_comp'])):
_set_frame(frag)
frags.append(frag)
# if the query is protein, we need to change the hit and query sequences
# from three-letter amino acid codes to one letter, and adjust their
# coordinates accordingly
if len(frags[0].aln_annotation) == 2: # 2 annotations == protein query
frags = _adjust_aa_seq(frags)
hsp = HSP(frags)
# set hsp-specific attributes
for attr in ('score', 'hit_split_codons', 'query_split_codons',
'model', 'vulgar_comp', 'cigar_comp', 'alphabet'):
if attr in hspd:
setattr(hsp, attr, hspd[attr])
return hsp
def _set_qresult_hits(qresult, hit_rows=[]):
"""Helper function for appending Hits without alignments into QueryResults."""
for hit_row in hit_rows:
hit_id, remainder = hit_row.split(' ', 1)
# TODO: parse hit and hsp properties properly; by dealing with:
# - any character in the description (brackets, spaces, etc.)
# - possible [f] or [r] presence (for frame info)
# - possible presence of E2() column
# - possible incomplete hit_id due to column length limit
# The current method only looks at the Hit ID, none of the things above
if hit_id not in qresult:
frag = HSPFragment(hit_id, qresult.id)
hsp = HSP([frag])
hit = Hit([hsp])
qresult.append(hit)
return qresult
def _parse_hit(self, query_id):
while True:
self.line = self.handle.readline()
if self.line.startswith('>>'):
break
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 _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_hsp(self, root_hsp_frag_elem, query_id, hit_id):
"""Iterator that transforms Hit_hsps XML elements into HSP objects.
Arguments:
root_hsp_frag_elem -- Element object of the Hit_hsps tag.
query_id -- Query ID string.
hit_id -- Hit ID string.
"""
# Hit_hsps DTD:
# <!ELEMENT Hsp (
# Hsp_num,
# Hsp_bit-score,
# Hsp_score,
# Hsp_evalue,
# Hsp_query-from,
# Hsp_query-to,
# Hsp_hit-from,
# Hsp_hit-to,
# Hsp_pattern-from?,
# Hsp_pattern-to?,
# Hsp_query-frame?,
# Hsp_hit-frame?,
# Hsp_identity?,
# Hsp_positive?,
# Hsp_gaps?,
# Hsp_align-len?,
# Hsp_density?,
# Hsp_qseq,
# Hsp_hseq,
# Hsp_midline?)>
# if value is None, feed the loop below an empty list
if root_hsp_frag_elem is None:
root_hsp_frag_elem = []
for hsp_frag_elem in root_hsp_frag_elem:
coords = {} # temporary container for coordinates
frag = HSPFragment(hit_id, query_id)
for key, val_info in _ELEM_FRAG.items():
value = hsp_frag_elem.findtext(key)
caster = val_info[1]
# adjust 'from' and 'to' coordinates to 0-based ones
if value is not None:
if key.endswith('-from') or key.endswith('-to'):
# store coordinates for further processing
coords[val_info[0]] = caster(value)
continue
# recast only if value is not intended to be str
elif caster is not str:
value = caster(value)
setattr(frag, val_info[0], value)
# set the similarity characters into aln_annotation dict
frag.aln_annotation['similarity'] = \
hsp_frag_elem.findtext('Hsp_midline')
# process coordinates
# since 'x-from' could be bigger than 'x-to', we need to figure
# out which one is smaller/bigger since 'x_start' is always smaller
# than 'x_end'
for coord_type in ('query', 'hit', 'pattern'):
start_type = coord_type + '_start'
end_type = coord_type + '_end'
try:
start = coords[start_type]
end = coords[end_type]
except KeyError:
continue
else:
# convert to python range and setattr
setattr(frag, start_type, min(start, end) - 1)
setattr(frag, end_type, max(start, end))
# set alphabet, based on program
prog = self._meta.get('program')
if prog == 'blastn':
frag.alphabet = generic_dna
elif prog in ['blastp', 'blastx', 'tblastn', 'tblastx']:
frag.alphabet = generic_protein
hsp = HSP([frag])
for key, val_info in _ELEM_HSP.items():
value = hsp_frag_elem.findtext(key)
caster = val_info[1]
if value is not None:
if caster is not str:
value = caster(value)
setattr(hsp, val_info[0], value)
# delete element after we finish parsing it
hsp_frag_elem.clear()
yield hsp
def _create_hits(self, hit_attrs, qid, qdesc):
"""Parses a HMMER3 hsp block, beginning with the hsp table."""
# read through until the beginning of the hsp block
self._read_until(lambda line: line.startswith('Internal pipeline') or
line.startswith('>>'))
# start parsing the hsp block
hit_list = []
while True:
if self.line.startswith('Internal pipeline'):
# by this time we should've emptied the hit attr list
assert len(hit_attrs) == 0
return hit_list
assert self.line.startswith('>>')
hid, hdesc = self.line[len('>> '):].split(' ', 1)
# read through the hsp table header and move one more line
self._read_until(lambda line:
line.startswith(' --- ------ ----- --------') or \
line.startswith(' [No individual domains'))
self.line = read_forward(self.handle)
# parse the hsp table for the current hit
hsp_list = []
while True:
# break out of hsp parsing if there are no hits, it's the last hsp
# or it's the start of a new hit
if self.line.startswith(' [No targets detected that satisfy') or \
self.line.startswith(' [No individual domains') or \
self.line.startswith('Internal pipeline statistics summary:') or \
self.line.startswith(' Alignments for each domain:') or \
self.line.startswith('>>'):
hit_attr = hit_attrs.pop(0)
hit = Hit(hsp_list)
for attr, value in hit_attr.items():
setattr(hit, attr, value)
if not hit:
hit.query_description = qdesc
hit_list.append(hit)
break
parsed = [x for x in self.line.strip().split(' ') if x]
assert len(parsed) == 16
# parsed column order:
# index, is_included, bitscore, bias, evalue_cond, evalue
# hmmfrom, hmmto, query_ends, hit_ends, alifrom, alito,
# envfrom, envto, acc_avg
frag = HSPFragment(hid, qid)
# HMMER3 alphabets are always protein alphabets
frag.alphabet = generic_protein
# depending on whether the program is hmmsearch, hmmscan, or phmmer
# {hmm,ali}{from,to} can either be hit_{from,to} or query_{from,to}
# for hmmscan, hit is the hmm profile, query is the sequence
if self._meta.get('program') == 'hmmscan':
# adjust 'from' and 'to' coordinates to 0-based ones
frag.hit_start = int(parsed[6]) - 1
frag.hit_end = int(parsed[7])
frag.query_start = int(parsed[9]) - 1
frag.query_end = int(parsed[10])
elif self._meta.get('program') in ['hmmsearch', 'phmmer']:
# adjust 'from' and 'to' coordinates to 0-based ones
frag.hit_start = int(parsed[9]) - 1
frag.hit_end = int(parsed[10])
frag.query_start = int(parsed[6]) - 1
frag.query_end = int(parsed[7])
# strand is always 0, since HMMER now only handles protein
frag.hit_strand = frag.query_strand = 0
hsp = HSP([frag])
hsp.domain_index = int(parsed[0])
hsp.is_included = parsed[1] == '!'
hsp.bitscore = float(parsed[2])
hsp.bias = float(parsed[3])
hsp.evalue_cond = float(parsed[4])
hsp.evalue = float(parsed[5])
if self._meta.get('program') == 'hmmscan':
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.hit_endtype = parsed[8]
hsp.query_endtype = parsed[11]
elif self._meta.get('program') in ['hmmsearch', 'phmmer']:
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.hit_endtype = parsed[11]
hsp.query_endtype = parsed[8]
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.env_start = int(parsed[12]) - 1
hsp.env_end = int(parsed[13])
hsp.env_endtype = parsed[14]
hsp.acc_avg = float(parsed[15])
hsp_list.append(hsp)
self.line = read_forward(self.handle)
# parse the hsp alignments
if self.line.startswith(' Alignments for each domain:'):
self._parse_aln_block(hid, hit.hsps)
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 _create_hits(self, hit_attrs, qid, qdesc):
"""Parses a HMMER3 hsp block, beginning with the hsp table."""
# read through until the beginning of the hsp block
self._read_until(lambda line: line.startswith("Internal pipeline") or line.startswith(">>"))
# start parsing the hsp block
hit_list = []
while True:
if self.line.startswith("Internal pipeline"):
# by this time we should've emptied the hit attr list
assert len(hit_attrs) == 0
return hit_list
assert self.line.startswith(">>")
hid, hdesc = self.line[len(">> ") :].split(" ", 1)
# read through the hsp table header and move one more line
self._read_until(
lambda line: line.startswith(" --- ------ ----- --------")
or line.startswith(" [No individual domains")
)
self.line = read_forward(self.handle)
# parse the hsp table for the current hit
hsp_list = []
while True:
# break out of hsp parsing if there are no hits, it's the last hsp
# or it's the start of a new hit
if (
self.line.startswith(" [No targets detected that satisfy")
or self.line.startswith(" [No individual domains")
or self.line.startswith("Internal pipeline statistics summary:")
or self.line.startswith(" Alignments for each domain:")
or self.line.startswith(">>")
):
hit_attr = hit_attrs.pop(0)
hit = Hit(hsp_list)
for attr, value in hit_attr.items():
setattr(hit, attr, value)
if not hit:
hit.query_description = qdesc
hit_list.append(hit)
break
parsed = [x for x in self.line.strip().split(" ") if x]
assert len(parsed) == 16
# parsed column order:
# index, is_included, bitscore, bias, evalue_cond, evalue
# hmmfrom, hmmto, query_ends, hit_ends, alifrom, alito,
# envfrom, envto, acc_avg
frag = HSPFragment(hid, qid)
# HMMER3 alphabets are always protein alphabets
frag.alphabet = generic_protein
# depending on whether the program is hmmsearch, hmmscan, or phmmer
# {hmm,ali}{from,to} can either be hit_{from,to} or query_{from,to}
# for hmmscan, hit is the hmm profile, query is the sequence
if self._meta.get("program") == "hmmscan":
# adjust 'from' and 'to' coordinates to 0-based ones
frag.hit_start = int(parsed[6]) - 1
frag.hit_end = int(parsed[7])
frag.query_start = int(parsed[9]) - 1
frag.query_end = int(parsed[10])
elif self._meta.get("program") in ["hmmsearch", "phmmer"]:
# adjust 'from' and 'to' coordinates to 0-based ones
frag.hit_start = int(parsed[9]) - 1
frag.hit_end = int(parsed[10])
frag.query_start = int(parsed[6]) - 1
frag.query_end = int(parsed[7])
# strand is always 0, since HMMER now only handles protein
frag.hit_strand = frag.query_strand = 0
hsp = HSP([frag])
hsp.domain_index = int(parsed[0])
hsp.is_included = parsed[1] == "!"
hsp.bitscore = float(parsed[2])
hsp.bias = float(parsed[3])
hsp.evalue_cond = float(parsed[4])
hsp.evalue = float(parsed[5])
if self._meta.get("program") == "hmmscan":
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.hit_endtype = parsed[8]
hsp.query_endtype = parsed[11]
elif self._meta.get("program") in ["hmmsearch", "phmmer"]:
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.hit_endtype = parsed[11]
hsp.query_endtype = parsed[8]
# adjust 'from' and 'to' coordinates to 0-based ones
hsp.env_start = int(parsed[12]) - 1
hsp.env_end = int(parsed[13])
hsp.env_endtype = parsed[14]
hsp.acc_avg = float(parsed[15])
hsp_list.append(hsp)
self.line = read_forward(self.handle)
# parse the hsp alignments
if self.line.startswith(" Alignments for each domain:"):
self._parse_aln_block(hid, hit.hsps)
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 _create_hsp(hid, qid, psl):
# protein flag
is_protein = _is_protein(psl)
# strand
#if query is protein, strand is 0
if is_protein:
qstrand = 0
else:
qstrand = 1 if psl['strand'][0] == '+' else -1
# try to get hit strand, if it exists
try:
hstrand = 1 if psl['strand'][1] == '+' else -1
except IndexError:
hstrand = 1 # hit strand defaults to plus
# query block starts
qstarts = _reorient_starts(psl['qstarts'], psl['blocksizes'], psl['qsize'],
qstrand)
# hit block starts
if len(psl['strand']) == 2:
hstarts = _reorient_starts(psl['tstarts'], psl['blocksizes'],
psl['tsize'], hstrand)
else:
hstarts = psl['tstarts']
# set query and hit coords
# this assumes each block has no gaps (which seems to be the case)
assert len(qstarts) == len(hstarts) == len(psl['blocksizes'])
query_range_all = list(
zip(qstarts, [x + y for x, y in zip(qstarts, psl['blocksizes'])]))
hit_range_all = list(
zip(hstarts, [x + y for x, y in zip(hstarts, psl['blocksizes'])]))
# check length of sequences and coordinates, all must match
if 'tseqs' in psl and 'qseqs' in psl:
assert len(psl['tseqs']) == len(psl['qseqs']) == \
len(query_range_all) == len(hit_range_all)
else:
assert len(query_range_all) == len(hit_range_all)
frags = []
# iterating over query_range_all, but hit_range_all works just as well
for idx, qcoords in enumerate(query_range_all):
hseqlist = psl.get('tseqs')
hseq = '' if not hseqlist else hseqlist[idx]
qseqlist = psl.get('qseqs')
qseq = '' if not qseqlist else qseqlist[idx]
frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
# set alphabet
frag.alphabet = generic_dna
# set coordinates
frag.query_start = qcoords[0]
frag.query_end = qcoords[1]
frag.hit_start = hit_range_all[idx][0]
frag.hit_end = hit_range_all[idx][1]
# and strands
frag.query_strand = qstrand
frag.hit_strand = hstrand
frags.append(frag)
# create hsp object
hsp = HSP(frags)
# check if start and end are set correctly
assert hsp.query_start == psl['qstart']
assert hsp.query_end == psl['qend']
assert hsp.hit_start == psl['tstart']
assert hsp.hit_end == psl['tend']
# and check block spans as well
assert hsp.query_span_all == hsp.hit_span_all == psl['blocksizes']
# set its attributes
hsp.match_num = psl['matches']
hsp.mismatch_num = psl['mismatches']
hsp.match_rep_num = psl['repmatches']
hsp.n_num = psl['ncount']
hsp.query_gapopen_num = psl['qnuminsert']
hsp.query_gap_num = psl['qbaseinsert']
hsp.hit_gapopen_num = psl['tnuminsert']
hsp.hit_gap_num = psl['tbaseinsert']
hsp.ident_num = psl['matches'] + psl['repmatches']
hsp.gapopen_num = psl['qnuminsert'] + psl['tnuminsert']
hsp.gap_num = psl['qbaseinsert'] + psl['tbaseinsert']
hsp.query_is_protein = is_protein
hsp.ident_pct = 100.0 - _calc_millibad(psl, is_protein) * 0.1
hsp.score = _calc_score(psl, is_protein)
# helper flag, for writing
hsp._has_hit_strand = len(psl['strand']) == 2
return hsp
def _parse_hsp(self, root_hsp_frag_elem, query_id, hit_id):
"""Iterator that transforms Hit_hsps XML elements into HSP objects.
Arguments:
root_hsp_frag_elem -- Element object of the Hit_hsps tag.
query_id -- Query ID string.
hit_id -- Hit ID string.
"""
# Hit_hsps DTD:
# <!ELEMENT Hsp (
# Hsp_num,
# Hsp_bit-score,
# Hsp_score,
# Hsp_evalue,
# Hsp_query-from,
# Hsp_query-to,
# Hsp_hit-from,
# Hsp_hit-to,
# Hsp_pattern-from?,
# Hsp_pattern-to?,
# Hsp_query-frame?,
# Hsp_hit-frame?,
# Hsp_identity?,
# Hsp_positive?,
# Hsp_gaps?,
# Hsp_align-len?,
# Hsp_density?,
# Hsp_qseq,
# Hsp_hseq,
# Hsp_midline?)>
# if value is None, feed the loop below an empty list
if root_hsp_frag_elem is None:
root_hsp_frag_elem = []
for hsp_frag_elem in root_hsp_frag_elem:
coords = {} # temporary container for coordinates
frag = HSPFragment(hit_id, query_id)
for key, val_info in _ELEM_FRAG.items():
value = hsp_frag_elem.findtext(key)
caster = val_info[1]
# adjust 'from' and 'to' coordinates to 0-based ones
if value is not None:
if key.endswith('-from') or key.endswith('-to'):
# store coordinates for further processing
coords[val_info[0]] = caster(value)
continue
# recast only if value is not intended to be str
elif caster is not str:
value = caster(value)
setattr(frag, val_info[0], value)
# set the similarity characters into aln_annotation dict
frag.aln_annotation['similarity'] = \
hsp_frag_elem.findtext('Hsp_midline')
# process coordinates
# since 'x-from' could be bigger than 'x-to', we need to figure
# out which one is smaller/bigger since 'x_start' is always smaller
# than 'x_end'
for coord_type in ('query', 'hit', 'pattern'):
start_type = coord_type + '_start'
end_type = coord_type + '_end'
try:
start = coords[start_type]
end = coords[end_type]
except KeyError:
continue
else:
# convert to python range and setattr
setattr(frag, start_type, min(start, end) - 1)
setattr(frag, end_type, max(start, end))
# set alphabet, based on program
prog = self._meta.get('program')
if prog == 'blastn':
frag.alphabet = generic_dna
elif prog in ['blastp', 'blastx', 'tblastn', 'tblastx']:
frag.alphabet = generic_protein
hsp = HSP([frag])
for key, val_info in _ELEM_HSP.items():
value = hsp_frag_elem.findtext(key)
caster = val_info[1]
if value is not None:
if caster is not str:
value = caster(value)
setattr(hsp, val_info[0], value)
# delete element after we finish parsing it
hsp_frag_elem.clear()
yield hsp
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 _create_hsp(hid, qid, psl):
# protein flag
is_protein = _is_protein(psl)
# strand
#if query is protein, strand is 0
if is_protein:
qstrand = 0
else:
qstrand = 1 if psl['strand'][0] == '+' else -1
# try to get hit strand, if it exists
try:
hstrand = 1 if psl['strand'][1] == '+' else -1
except IndexError:
hstrand = 1 # hit strand defaults to plus
# query block starts
qstarts = _reorient_starts(psl['qstarts'],
psl['blocksizes'], psl['qsize'], qstrand)
# hit block starts
if len(psl['strand']) == 2:
hstarts = _reorient_starts(psl['tstarts'],
psl['blocksizes'], psl['tsize'], hstrand)
else:
hstarts = psl['tstarts']
# set query and hit coords
# this assumes each block has no gaps (which seems to be the case)
assert len(qstarts) == len(hstarts) == len(psl['blocksizes'])
query_range_all = list(zip(qstarts, [x + y for x, y in
zip(qstarts, psl['blocksizes'])]))
hit_range_all = list(zip(hstarts, [x + y for x, y in
zip(hstarts, psl['blocksizes'])]))
# check length of sequences and coordinates, all must match
if 'tseqs' in psl and 'qseqs' in psl:
assert len(psl['tseqs']) == len(psl['qseqs']) == \
len(query_range_all) == len(hit_range_all)
else:
assert len(query_range_all) == len(hit_range_all)
frags = []
# iterating over query_range_all, but hit_range_all works just as well
for idx, qcoords in enumerate(query_range_all):
hseqlist = psl.get('tseqs')
hseq = '' if not hseqlist else hseqlist[idx]
qseqlist = psl.get('qseqs')
qseq = '' if not qseqlist else qseqlist[idx]
frag = HSPFragment(hid, qid, hit=hseq, query=qseq)
# set alphabet
frag.alphabet = generic_dna
# set coordinates
frag.query_start = qcoords[0]
frag.query_end = qcoords[1]
frag.hit_start = hit_range_all[idx][0]
frag.hit_end = hit_range_all[idx][1]
# and strands
frag.query_strand = qstrand
frag.hit_strand = hstrand
frags.append(frag)
# create hsp object
hsp = HSP(frags)
# check if start and end are set correctly
assert hsp.query_start == psl['qstart']
assert hsp.query_end == psl['qend']
assert hsp.hit_start == psl['tstart']
assert hsp.hit_end == psl['tend']
# and check block spans as well
assert hsp.query_span_all == hsp.hit_span_all == psl['blocksizes']
# set its attributes
hsp.match_num = psl['matches']
hsp.mismatch_num = psl['mismatches']
hsp.match_rep_num = psl['repmatches']
hsp.n_num = psl['ncount']
hsp.query_gapopen_num = psl['qnuminsert']
hsp.query_gap_num = psl['qbaseinsert']
hsp.hit_gapopen_num = psl['tnuminsert']
hsp.hit_gap_num = psl['tbaseinsert']
hsp.ident_num = psl['matches'] + psl['repmatches']
hsp.gapopen_num = psl['qnuminsert'] + psl['tnuminsert']
hsp.gap_num = psl['qbaseinsert'] + psl['tbaseinsert']
hsp.query_is_protein = is_protein
hsp.ident_pct = 100.0 - _calc_millibad(psl, is_protein) * 0.1
hsp.score = _calc_score(psl, is_protein)
# helper flag, for writing
hsp._has_hit_strand = len(psl['strand']) == 2
return hsp
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_hsps(self, hit_placeholders):
"""Parse a HMMER2 hsp block, beginning with the hsp table."""
# HSPs may occur in different order than the hits
# so store Hit objects separately first
unordered_hits = {}
while self.read_next():
if self.line.startswith('Alignments') or \
self.line.startswith('Histogram') or \
self.line == '//':
break
if self.line.startswith('Model') or \
self.line.startswith('Sequence') or \
self.line.startswith('--------'):
continue
id_, domain, seq_f, seq_t, seq_compl, hmm_f, hmm_t, hmm_compl, \
score, evalue = self.line.split()
frag = HSPFragment(id_, self.qresult.id)
frag.alphabet = generic_protein
if self._meta['program'] == 'hmmpfam':
frag.hit_start = int(hmm_f) - 1
frag.hit_end = int(hmm_t)
frag.query_start = int(seq_f) - 1
frag.query_end = int(seq_t)
elif self._meta['program'] == 'hmmsearch':
frag.query_start = int(hmm_f) - 1
frag.query_end = int(hmm_t)
frag.hit_start = int(seq_f) - 1
frag.hit_end = int(seq_t)
hsp = HSP([frag])
hsp.evalue = float(evalue)
hsp.bitscore = float(score)
hsp.domain_index = int(domain.split('/')[0])
if self._meta['program'] == 'hmmpfam':
hsp.hit_endtype = hmm_compl
hsp.query_endtype = seq_compl
elif self._meta['program'] == 'hmmsearch':
hsp.query_endtype = hmm_compl
hsp.hit_endtype = seq_compl
if id_ not in unordered_hits:
placeholder = [ p for p in hit_placeholders if p.id_ == id_][0]
hit = placeholder.createHit([hsp])
unordered_hits[id_] = hit
else:
hit = unordered_hits[id_]
hsp.hit_description = hit.description
hit.append(hsp)
# The placeholder list is in the correct order, so use that order for
# the Hit objects in the qresult
for p in hit_placeholders:
self.qresult.append(unordered_hits[p.id_])