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# Copyright 2003 Iddo Friedberg. 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.
"""A parser for the NCBI blastpgp version 2.2.5 output format.
Currently only supports the '-m 9' option, (table w/ annotations).
Returns a BlastTableRec instance
"""
class BlastTableEntry:
"""Container for Blast Table Entry, the field values from the table."""
def __init__(self, in_rec):
"""Initialize the class."""
bt_fields = in_rec.split()
self.qid = bt_fields[0].split("|")
self.sid = bt_fields[1].split("|")
self.pid = float(bt_fields[2])
self.ali_len = int(bt_fields[3])
self.mis = int(bt_fields[4])
self.gaps = int(bt_fields[5])
self.q_bounds = (int(bt_fields[6]), int(bt_fields[7]))
self.s_bounds = (int(bt_fields[8]), int(bt_fields[9]))
self.e_value = float(bt_fields[10])
self.bit_score = float(bt_fields[11])
class BlastTableRec:
"""Container for Blast Table record, list of Blast Table Entries."""
def __init__(self):
"""Initialize the class."""
self.program = None
self.version = None
self.date = None
self.iteration = None
self.query = None
self.database = None
self.entries = []
def add_entry(self, entry):
"""Add entry to Blast Table."""
self.entries.append(entry)
class BlastTableReader:
"""Reader for the output of blastpgp."""
reader_keywords = {
"BLASTP": "version",
"Iteration": "iteration",
"Query": "query",
"Database": "database",
"Fields": "fields",
}
def __init__(self, handle):
"""Initialize the class."""
self.handle = handle
inline = self.handle.readline()
# zip forward to start of record
while inline and "BLASTP" not in inline:
inline = self.handle.readline()
self._lookahead = inline
self._n = 0
self._in_header = 1
def __next__(self):
"""Return the next record when iterating over the file."""
self.table_record = BlastTableRec()
self._n += 1
inline = self._lookahead
if not inline:
return None
while inline:
if inline[0] == "#":
if self._in_header:
self._in_header = self._consume_header(inline)
else:
break
else:
self._consume_entry(inline)
self._in_header = 0
inline = self.handle.readline()
self._lookahead = inline
self._in_header = 1
return self.table_record
def _consume_entry(self, inline):
current_entry = BlastTableEntry(inline)
self.table_record.add_entry(current_entry)
def _consume_header(self, inline):
for keyword in self.reader_keywords:
if keyword in inline:
return self._Parse("_parse_%s" % self.reader_keywords[keyword], inline)
def _parse_version(self, inline):
program, version, date = inline.split()[1:]
self.table_record.program = program
self.table_record.version = version
self.table_record.date = date
return 1
def _parse_iteration(self, inline):
self.table_record.iteration = int(inline.split()[2])
return 1
def _parse_query(self, inline):
self.table_record.query = inline.split()[2:]
return 1
def _parse_database(self, inline):
self.table_record.database = inline.split()[2]
return 1
def _parse_fields(self, inline):
return 0
def _Parse(self, method_name, inline):
return getattr(self, method_name)(inline)
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