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# Copyright 2012 by Wibowo Arindrarto. 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 table output format."""
from itertools import chain
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
__all__ = ("Hmmer3TabParser", "Hmmer3TabIndexer", "Hmmer3TabWriter")
class Hmmer3TabParser:
"""Parser for the HMMER table format."""
def __init__(self, handle):
"""Initialize the class."""
self.handle = handle
self.line = self.handle.readline()
def __iter__(self):
"""Iterate over Hmmer3TabParser, yields query results."""
header_mark = "#"
# read through the header if it exists
while self.line.startswith(header_mark):
self.line = self.handle.readline()
# if we have result rows, parse it
if self.line:
yield from self._parse_qresult()
def _parse_row(self):
"""Return a dictionary of parsed row values (PRIVATE)."""
cols = [x for x in self.line.strip().split(" ") if x]
if len(cols) < 18:
raise ValueError("Less columns than expected, only %i" % len(cols))
# if len(cols) > 19, we have extra description columns
# combine them all into one string in the 19th column
cols[18] = " ".join(cols[18:])
# assign parsed column data into qresult, hit, and hsp dicts
qresult = {}
qresult["id"] = cols[2] # query name
qresult["accession"] = cols[3] # query accession
hit = {}
hit["id"] = cols[0] # target name
hit["accession"] = cols[1] # target accession
hit["evalue"] = float(cols[4]) # evalue (full sequence)
hit["bitscore"] = float(cols[5]) # score (full sequence)
hit["bias"] = float(cols[6]) # bias (full sequence)
hit["domain_exp_num"] = float(cols[10]) # exp
hit["region_num"] = int(cols[11]) # reg
hit["cluster_num"] = int(cols[12]) # clu
hit["overlap_num"] = int(cols[13]) # ov
hit["env_num"] = int(cols[14]) # env
hit["domain_obs_num"] = int(cols[15]) # dom
hit["domain_reported_num"] = int(cols[16]) # rep
hit["domain_included_num"] = int(cols[17]) # inc
hit["description"] = cols[18] # description of target
hsp = {}
hsp["evalue"] = float(cols[7]) # evalue (best 1 domain)
hsp["bitscore"] = float(cols[8]) # score (best 1 domain)
hsp["bias"] = float(cols[9]) # bias (best 1 domain)
# strand is always 0, since HMMER now only handles protein
frag = {}
frag["hit_strand"] = frag["query_strand"] = 0
frag["molecule_type"] = "protein"
return {"qresult": qresult, "hit": hit, "hsp": hsp, "frag": frag}
def _parse_qresult(self):
"""Return QueryResult objects (PRIVATE)."""
# 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 = []
cur_qid = None
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()
class Hmmer3TabIndexer(SearchIndexer):
"""Indexer class for HMMER table output."""
_parser = Hmmer3TabParser
# denotes column location for query identifier
_query_id_idx = 2
def __iter__(self):
"""Iterate over the file handle; yields key, start offset, and length."""
handle = self._handle
handle.seek(0)
query_id_idx = self._query_id_idx
qresult_key = None
header_mark = b"#"
split_mark = b" "
# set line with initial mock value, to emulate header
line = header_mark
# read through header
while line.startswith(header_mark):
start_offset = handle.tell()
line = handle.readline()
# and index the qresults
while True:
end_offset = handle.tell()
if not line:
break
cols = [x for x in line.strip().split(split_mark) if x]
if qresult_key is None:
qresult_key = cols[query_id_idx]
else:
curr_key = cols[query_id_idx]
if curr_key != qresult_key:
adj_end = end_offset - len(line)
yield (qresult_key.decode(), start_offset, adj_end - start_offset)
qresult_key = curr_key
start_offset = adj_end
line = handle.readline()
if not line:
yield (qresult_key.decode(), start_offset, end_offset - start_offset)
break
def get_raw(self, offset):
"""Return the raw bytes string of a QueryResult object from the given offset."""
handle = self._handle
handle.seek(offset)
query_id_idx = self._query_id_idx
qresult_key = None
qresult_raw = b""
split_mark = b" "
while True:
line = handle.readline()
if not line:
break
cols = [x for x in line.strip().split(split_mark) if x]
if qresult_key is None:
qresult_key = cols[query_id_idx]
else:
curr_key = cols[query_id_idx]
if curr_key != qresult_key:
break
qresult_raw += line
return qresult_raw
class Hmmer3TabWriter:
"""Writer for hmmer3-tab output format."""
def __init__(self, handle):
"""Initialize the class."""
self.handle = handle
def write_file(self, qresults):
"""Write to the handle.
Returns a tuple of how many QueryResult, Hit, and HSP objects were written.
"""
handle = self.handle
qresult_counter, hit_counter, hsp_counter, frag_counter = 0, 0, 0, 0
try:
first_qresult = next(qresults)
except StopIteration:
handle.write(self._build_header())
else:
# write header
handle.write(self._build_header(first_qresult))
# and then the qresults
for qresult in chain([first_qresult], qresults):
if qresult:
handle.write(self._build_row(qresult))
qresult_counter += 1
hit_counter += len(qresult)
hsp_counter += sum(len(hit) for hit in qresult)
frag_counter += sum(len(hit.fragments) for hit in qresult)
return qresult_counter, hit_counter, hsp_counter, frag_counter
def _build_header(self, first_qresult=None):
"""Return the header string of a HMMER table output (PRIVATE)."""
# calculate whitespace required
# adapted from HMMER's source: src/p7_tophits.c#L1083
if first_qresult is not None:
# qnamew = max(20, len(first_qresult.id))
qnamew = 20 # why doesn't the above work?
tnamew = max(20, len(first_qresult[0].id))
qaccw = max(10, len(first_qresult.accession))
taccw = max(10, len(first_qresult[0].accession))
else:
qnamew, tnamew, qaccw, taccw = 20, 20, 10, 10
# Turn black code style off
# fmt: off
header = ("#%*s %22s %22s %33s\n"
% (tnamew + qnamew + taccw + qaccw + 2, "",
"--- full sequence ----", "--- best 1 domain ----",
"--- domain number estimation ----"))
header += ("#%-*s %-*s %-*s %-*s %9s %6s %5s %9s %6s %5s %5s %3s "
"%3s %3s %3s %3s %3s %3s %s\n"
% (tnamew - 1, " target name",
taccw, "accession", qnamew, "query name", qaccw,
"accession", " E-value", " score", " bias",
" E-value", " score", " bias", "exp",
"reg", "clu", " ov", "env", "dom", "rep",
"inc", "description of target"))
header += ("#%*s %*s %*s %*s %9s %6s %5s %9s %6s %5s %5s %3s %3s "
"%3s %3s %3s %3s %3s %s\n"
% (tnamew - 1, "-------------------",
taccw, "----------", qnamew, "--------------------", qaccw,
"----------", "---------", "------", "-----", "---------",
"------", "-----", "---", "---", "---", "---", "---", "---",
"---", "---", "---------------------"))
# Turn black code style on
# fmt: on
return header
def _build_row(self, qresult):
"""Return a string or one row or more of the QueryResult object (PRIVATE)."""
rows = ""
# calculate whitespace required
# adapted from HMMER's source: src/p7_tophits.c#L1083
qnamew = max(20, len(qresult.id))
tnamew = max(20, len(qresult[0].id))
qaccw = max(10, len(qresult.accession))
taccw = max(10, len(qresult[0].accession))
for hit in qresult:
rows += (
"%-*s %-*s %-*s %-*s %9.2g %6.1f %5.1f %9.2g %6.1f"
" %5.1f %5.1f %3d %3d %3d %3d %3d %3d %3d %s\n"
% (
tnamew,
hit.id,
taccw,
hit.accession,
qnamew,
qresult.id,
qaccw,
qresult.accession,
hit.evalue,
hit.bitscore,
hit.bias,
hit.hsps[0].evalue,
hit.hsps[0].bitscore,
hit.hsps[0].bias,
hit.domain_exp_num,
hit.region_num,
hit.cluster_num,
hit.overlap_num,
hit.env_num,
hit.domain_obs_num,
hit.domain_reported_num,
hit.domain_included_num,
hit.description,
)
)
return rows
# if not used as a module, run the doctest
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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