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# Copyright 2012 by Kai Blin. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser for HMMER 2 text output."""
import re
from Bio.SearchIO._utils import read_forward
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
from ._base import _BaseHmmerTextIndexer
__all__ = ("Hmmer2TextParser", "Hmmer2TextIndexer")
_HSP_ALIGN_LINE = re.compile(r"(\S+):\s+domain (\d+) of (\d+)")
class _HitPlaceholder:
def createHit(self, hsp_list):
hit = Hit(hsp_list)
hit.id_ = self.id_
hit.evalue = self.evalue
hit.bitscore = self.bitscore
if self.description:
hit.description = self.description
hit.domain_obs_num = self.domain_obs_num
return hit
class Hmmer2TextParser:
"""Iterator for the HMMER 2.0 text output."""
def __init__(self, handle):
"""Initialize the class."""
self.handle = handle
self.buf = []
self._meta = self.parse_preamble()
def __iter__(self):
"""Iterate over Hmmer2TextParser, yields query results."""
for qresult in self.parse_qresult():
qresult.program = self._meta.get("program")
qresult.target = self._meta.get("target")
qresult.version = self._meta.get("version")
yield qresult
def read_next(self, rstrip=True):
"""Return the next non-empty line, trailing whitespace removed."""
if len(self.buf) > 0:
return self.buf.pop()
self.line = self.handle.readline()
while self.line and rstrip and not self.line.strip():
self.line = self.handle.readline()
if self.line:
if rstrip:
self.line = self.line.rstrip()
return self.line
def push_back(self, line):
"""Un-read a line that should not be parsed yet."""
self.buf.append(line)
def parse_key_value(self):
"""Parse key-value pair separated by colon."""
key, value = self.line.split(":", 1)
return key.strip(), value.strip()
def parse_preamble(self):
"""Parse HMMER2 preamble."""
meta = {}
state = "GENERIC"
while self.read_next():
if state == "GENERIC":
if self.line.startswith("hmm"):
meta["program"] = self.line.split("-")[0].strip()
elif self.line.startswith("HMMER is"):
continue
elif self.line.startswith("HMMER"):
meta["version"] = self.line.split()[1]
elif self.line.count("-") == 36:
state = "OPTIONS"
continue
assert state == "OPTIONS"
assert "program" in meta
if self.line.count("-") == 32:
break
key, value = self.parse_key_value()
if meta["program"] == "hmmsearch":
if key == "Sequence database":
meta["target"] = value
continue
elif meta["program"] == "hmmpfam":
if key == "HMM file":
meta["target"] = value
continue
meta[key] = value
return meta
def parse_qresult(self):
"""Parse a HMMER2 query block."""
while self.read_next():
if not self.line.startswith("Query"):
return
_, 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_hits(self):
"""Parse a HMMER2 hit block, beginning with the hit table."""
hit_placeholders = []
while self.read_next():
if self.line.startswith("Parsed"):
break
if self.line.find("no hits") > -1:
break
if (
self.line.startswith("Sequence")
or self.line.startswith("Model")
or self.line.startswith("-------- ")
):
continue
fields = self.line.split()
id_ = fields.pop(0)
domain_obs_num = int(fields.pop())
evalue = float(fields.pop())
bitscore = float(fields.pop())
description = " ".join(fields).strip()
hit = _HitPlaceholder()
hit.id_ = id_
hit.evalue = evalue
hit.bitscore = bitscore
hit.description = description
hit.domain_obs_num = domain_obs_num
hit_placeholders.append(hit)
return hit_placeholders
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.molecule_type = "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_])
def parse_hsp_alignments(self):
"""Parse a HMMER2 HSP alignment block."""
if not self.line.startswith("Alignments"):
return
while self.read_next():
if self.line == "//" or self.line.startswith("Histogram"):
break
match = re.search(_HSP_ALIGN_LINE, self.line)
if match is None:
continue
id_ = match.group(1)
idx = int(match.group(2))
num = int(match.group(3))
hit = self.qresult[id_]
if hit.domain_obs_num != num:
continue
frag = hit[idx - 1][0]
hmmseq = ""
consensus = ""
otherseq = ""
structureseq = ""
pad = 0
while self.read_next() and self.line.startswith(" "):
# if there's structure information, parse that
if self.line[16:18] == "CS":
structureseq += self.line[19:].strip()
if not self.read_next():
break
# skip the *-> start marker if it exists
if self.line[19:22] == "*->":
seq = self.line[22:]
pad = 3
else:
seq = self.line[19:]
pad = 0
hmmseq += seq
line_len = len(seq)
if not self.read_next(rstrip=False):
break
consensus += self.line[19 + pad : 19 + pad + line_len]
# If there's no consensus sequence, hmmer2 doesn't
# bother to put spaces here, so add extra padding
extra_padding = len(hmmseq) - len(consensus)
consensus += " " * extra_padding
if not self.read_next():
break
# if we have a line break in the end marker, we get a
# whitespace-only otherseq line, making split()[0] return
# the end coordinate. That'll be a -, which is a valid character
# in the sequence, meaning we can't just strip it.
parts = self.line[19:].split()
if len(parts) == 2:
otherseq += self.line[19:].split()[0].strip()
self.push_back(self.line)
# get rid of the end marker
if hmmseq.endswith("<-*"):
hmmseq = hmmseq[:-3]
consensus = consensus[:-3]
# add similarity sequence to annotation
frag.aln_annotation["similarity"] = consensus
# if there's structure information, add it to the fragment
if structureseq:
frag.aln_annotation["CS"] = structureseq
if self._meta["program"] == "hmmpfam":
frag.hit = hmmseq
frag.query = otherseq
else:
frag.hit = otherseq
frag.query = hmmseq
class Hmmer2TextIndexer(_BaseHmmerTextIndexer):
"""Indexer for hmmer2-text format."""
_parser = Hmmer2TextParser
qresult_start = b"Query"
# qresults_ends for hmmpfam and hmmsearch
# need to anticipate both since hmmsearch have different query end mark
qresult_end = b"//"
def __iter__(self):
"""Iterate over Hmmer2TextIndexer; yields query results' key, offsets, 0."""
handle = self._handle
handle.seek(0)
start_offset = handle.tell()
regex_id = re.compile(rb"Query\s*(?:sequence|HMM)?:\s*(.*)")
# determine flag for hmmsearch
is_hmmsearch = False
line = read_forward(handle)
if line.startswith(b"hmmsearch"):
is_hmmsearch = True
while True:
end_offset = handle.tell()
if line.startswith(self.qresult_start):
regx = re.search(regex_id, line)
qresult_key = regx.group(1).strip()
# qresult start offset is the offset of this line
# (starts with the start mark)
start_offset = end_offset - len(line)
elif line.startswith(self.qresult_end):
yield qresult_key.decode(), start_offset, 0
start_offset = end_offset
elif not line:
# HACK: since hmmsearch can only have one query result
if is_hmmsearch:
yield qresult_key.decode(), start_offset, 0
break
line = read_forward(handle)
# if not used as a module, run the doctest
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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