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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import functools
import contextlib
import pandas as pd
_possible_columns = {'qseqid': str, 'qgi': float, 'qacc': str, 'qaccver': str,
'qlen': float, 'sseqid': str, 'sallseqid': str,
'sgi': float, 'sallgi': float, 'sacc': str,
'saccver': str, 'sallacc': str, 'slen': float,
'qstart': float, 'qend': float, 'sstart': float,
'send': float, 'qseq': str, 'sseq': str,
'evalue': float, 'bitscore': float, 'score': float,
'length': float, 'pident': float, 'nident': float,
'mismatch': float, 'positive': float, 'gapopen': float,
'gaps': float, 'ppos': float, 'frames': str,
'qframe': float, 'sframe': float, 'btop': float,
'staxids': str, 'sscinames': str, 'scomnames': str,
'sblastnames': str, 'sskingdoms': str, 'stitle': str,
'salltitles': str, 'sstrand': str, 'qcovs': float,
'qcovhsp': float}
def _parse_blast_data(fh, columns, error, error_message, comment=None,
skiprows=None):
read_csv = functools.partial(pd.read_csv, na_values='N/A', sep='\t',
header=None, keep_default_na=False,
comment=comment, skiprows=skiprows)
# HACK for https://github.com/pandas-dev/pandas/issues/14418
# this avoids closing the `fh`, whose lifetime isn't the responsibility
# of this parser
with _noop_close(fh) as fh:
lineone = read_csv(fh, nrows=1)
if len(lineone.columns) != len(columns):
raise error(error_message % (len(columns), len(lineone.columns)))
fh.seek(0)
return read_csv(fh, names=columns, dtype=_possible_columns)
# HACK for https://github.com/pandas-dev/pandas/issues/14418
@contextlib.contextmanager
def _noop_close(fh):
backup = fh.close
fh.close = lambda: None
try:
yield fh
finally:
fh.close = backup
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