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|
"""
BLAST+7 format (:mod:`skbio.io.format.blast7`)
==============================================
.. currentmodule:: skbio.io.format.blast7
The BLAST+7 format (``blast+7``) stores the results of a BLAST [1]_ database
search. This format is produced by both BLAST+ output
format 7 and legacy BLAST output format 9. The results
are stored in a simple tabular format with headers. Values are separated by the
tab character.
An example BLAST+7-formatted file comparing two nucleotide sequences, taken
from [2]_ (tab characters represented by ``<tab>``):
.. code-block:: none
# BLASTN 2.2.18+
# Query: gi|1786181|gb|AE000111.1|AE000111
# Subject: ecoli
# Fields: query acc., subject acc., evalue, q. start, q. end, s. st\
art, s. end
# 5 hits found
AE000111<tab>AE000111<tab>0.0<tab>1<tab>10596<tab>1<tab>10596
AE000111<tab>AE000174<tab>8e-30<tab>5565<tab>5671<tab>6928<tab>6821
AE000111<tab>AE000394<tab>1e-27<tab>5587<tab>5671<tab>135<tab>219
AE000111<tab>AE000425<tab>6e-26<tab>5587<tab>5671<tab>8552<tab>8468
AE000111<tab>AE000171<tab>3e-24<tab>5587<tab>5671<tab>2214<tab>2130
Format Support
==============
**Has Sniffer: Yes**
**State: Experimental as of 0.4.1.**
+------+------+---------------------------------------------------------------+
|Reader|Writer| Object Class |
+======+======+===============================================================+
|Yes |No |:mod:`pandas.DataFrame` |
+------+------+---------------------------------------------------------------+
Format Specification
====================
There are two BLAST+7 file formats supported by scikit-bio: BLAST+ output
format 7 (``-outfmt 7``) and legacy BLAST output format 9 (``-m 9``). Both file
formats are structurally similar, with minor differences.
Example BLAST+ output format 7 file::
# BLASTP 2.2.31+
# Query: query1
# Subject: subject2
# Fields: q. start, q. end, s. start, s. end, identical, mismatches, sbjct\
frame, query acc.ver, subject acc.ver
# 2 hits found
1 8 3 10 8 0 1 query1 subject2
2 5 2 15 8 0 2 query1 subject2
.. note:: Database searches without hits may occur in BLAST+ output format 7
files. scikit-bio ignores these "empty" records:
.. code-block:: none
# BLASTP 2.2.31+
# Query: query1
# Subject: subject1
# 0 hits found
Example legacy BLAST output format 9 file:
.. code-block:: none
# BLASTN 2.2.3 [May-13-2002]
# Database: other_vertebrate
# Query: AF178033
# Fields:
Query id,Subject id,% identity,alignment length,mismatches,gap openings,q.\
start,q. end,s. start,s. end,e-value,bit score
AF178033 EMORG:AF178033 100.00 811 0 0 1 811 1 811 0.0 1566.6
AF178033 EMORG:AF031394 99.63 811 3 0 1 811 99 909 0.0 1542.8
.. note:: scikit-bio requires fields to be consistent within a file.
BLAST Column Types
------------------
The following column types are output by BLAST and supported by scikit-bio.
For more information on these column types, see :mod:`skbio.io.format.blast6`.
+-------------------+----------------------+
|Field Name |DataFrame Column Name |
+===================+======================+
|query id |qseqid |
+-------------------+----------------------+
|query gi |qgi |
+-------------------+----------------------+
|query acc. |qacc |
+-------------------+----------------------+
|query acc.ver |qaccver |
+-------------------+----------------------+
|query length |qlen |
+-------------------+----------------------+
|subject id |sseqid |
+-------------------+----------------------+
|subject ids |sallseqid |
+-------------------+----------------------+
|subject gi |sgi |
+-------------------+----------------------+
|subject gis |sallgi |
+-------------------+----------------------+
|subject acc. |sacc |
+-------------------+----------------------+
|subject acc.ver |saccver |
+-------------------+----------------------+
|subject accs |sallacc |
+-------------------+----------------------+
|subject length |slen |
+-------------------+----------------------+
|q\. start |qstart |
+-------------------+----------------------+
|q\. end |qend |
+-------------------+----------------------+
|s\. start |sstart |
+-------------------+----------------------+
|s\. end |send |
+-------------------+----------------------+
|query seq |qseq |
+-------------------+----------------------+
|subject seq |sseq |
+-------------------+----------------------+
|evalue |evalue |
+-------------------+----------------------+
|bit score |bitscore |
+-------------------+----------------------+
|score |score |
+-------------------+----------------------+
|alignment length |length |
+-------------------+----------------------+
|% identity |pident |
+-------------------+----------------------+
|identical |nident |
+-------------------+----------------------+
|mismatches |mismatch |
+-------------------+----------------------+
|positives |positive |
+-------------------+----------------------+
|gap opens |gapopen |
+-------------------+----------------------+
|gaps |gaps |
+-------------------+----------------------+
|% positives |ppos |
+-------------------+----------------------+
|query/sbjct frames |frames |
+-------------------+----------------------+
|query frame |qframe |
+-------------------+----------------------+
|sbjct frame |sframe |
+-------------------+----------------------+
|BTOP |btop |
+-------------------+----------------------+
|subject tax ids |staxids |
+-------------------+----------------------+
|subject sci names |sscinames |
+-------------------+----------------------+
|subject com names |scomnames |
+-------------------+----------------------+
|subject blast names|sblastnames |
+-------------------+----------------------+
|subject super king\|sskingdoms |
|doms | |
+-------------------+----------------------+
|subject title |stitle |
+-------------------+----------------------+
|subject strand |sstrand |
+-------------------+----------------------+
|subject titles |salltitles |
+-------------------+----------------------+
|% query coverage p\|qcovs |
|er subject | |
+-------------------+----------------------+
|% query coverage p\|qcovhsp |
|er hsp | |
+-------------------+----------------------+
Examples
========
Suppose we have a BLAST+7 file:
>>> from io import StringIO
>>> import skbio.io
>>> import pandas as pd
>>> fs = '\\n'.join([
... '# BLASTN 2.2.18+',
... '# Query: gi|1786181|gb|AE000111.1|AE000111',
... '# Database: ecoli',
... '# Fields: query acc., subject acc., evalue, q. start, q. end, s. st\
art, s. end',
... '# 5 hits found',
... 'AE000111\\tAE000111\\t0.0\\t1\\t10596\\t1\\t10596',
... 'AE000111\\tAE000174\\t8e-30\\t5565\\t5671\\t6928\\t6821',
... 'AE000111\\tAE000171\\t3e-24\\t5587\\t5671\\t2214\\t2130',
... 'AE000111\\tAE000425\\t6e-26\\t5587\\t5671\\t8552\\t8468'
... ])
>>> fh = StringIO(fs)
Read the file into a ``pd.DataFrame``:
>>> df = skbio.io.read(fh, into=pd.DataFrame)
>>> df # doctest: +NORMALIZE_WHITESPACE
qacc sacc evalue qstart qend sstart send
0 AE000111 AE000111 0.000000e+00 1.0 10596.0 1.0 10596.0
1 AE000111 AE000174 8.000000e-30 5565.0 5671.0 6928.0 6821.0
2 AE000111 AE000171 3.000000e-24 5587.0 5671.0 2214.0 2130.0
3 AE000111 AE000425 6.000000e-26 5587.0 5671.0 8552.0 8468.0
Suppose we have a legacy BLAST 9 file:
>>> from io import StringIO
>>> import skbio.io
>>> import pandas as pd
>>> fs = '\\n'.join([
... '# BLASTN 2.2.3 [May-13-2002]',
... '# Database: other_vertebrate',
... '# Query: AF178033',
... '# Fields: ',
... 'Query id,Subject id,% identity,alignment length,mismatches,gap openin\
gs,q. start,q. end,s. start,s. end,e-value,bit score',
... 'AF178033\\tEMORG:AF178033\\t100.00\\t811\\t0\\t0\\t1\\t811\\t1\\t81\
1\\t0.0\\t1566.6',
... 'AF178033\\tEMORG:AF178032\\t94.57\\t811\\t44\\t0\\t1\\t811\\t1\\t81\
1\\t0.0\\t1217.7',
... 'AF178033\\tEMORG:AF178031\\t94.82\\t811\\t42\\t0\\t1\\t811\\t1\\t81\
1\\t0.0\\t1233.5'
... ])
>>> fh = StringIO(fs)
Read the file into a ``pd.DataFrame``:
>>> df = skbio.io.read(fh, into=pd.DataFrame)
>>> df # doctest: +NORMALIZE_WHITESPACE
qseqid sseqid pident length mismatch gapopen qstart qend \\
0 AF178033 EMORG:AF178033 100.00 811.0 0.0 0.0 1.0 811.0
1 AF178033 EMORG:AF178032 94.57 811.0 44.0 0.0 1.0 811.0
2 AF178033 EMORG:AF178031 94.82 811.0 42.0 0.0 1.0 811.0
<BLANKLINE>
sstart send evalue bitscore
0 1.0 811.0 0.0 1566.6
1 1.0 811.0 0.0 1217.7
2 1.0 811.0 0.0 1233.5
References
==========
.. [1] Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990)
"Basic local alignment search tool." J. Mol. Biol. 215:403-410.
.. [2] http://www.ncbi.nlm.nih.gov/books/NBK279682/
"""
# ----------------------------------------------------------------------------
# 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 pandas as pd
from skbio.io import create_format, BLAST7FormatError
from skbio.io.format._blast import _parse_blast_data
blast7 = create_format('blast+7')
column_converter = {'query id': 'qseqid', 'query gi': 'qgi',
'query acc.': 'qacc', 'query acc.ver': 'qaccver',
'query length': 'qlen', 'subject id': 'sseqid',
'subject ids': 'sallseqid', 'subject gi': 'sgi',
'subject gis': 'sallgi', 'subject acc.': 'sacc',
'subject acc.ver': 'saccver', 'subject accs.': 'sallacc',
'subject length': 'slen', 'q. start': 'qstart',
'q. end': 'qend', 's. start': 'sstart', 's. end': 'send',
'query seq': 'qseq', 'subject seq': 'sseq',
'evalue': 'evalue', 'bit score': 'bitscore',
'score': 'score', 'alignment length': 'length',
'% identity': 'pident', 'identical': 'nident',
'mismatches': 'mismatch', 'positives': 'positive',
'gap opens': 'gapopen', 'gaps': 'gaps',
'% positives': 'ppos', 'query/sbjct frames': 'frames',
'query frame': 'qframe', 'sbjct frame': 'sframe',
'BTOP': 'btop', 'subject tax ids': 'staxids',
'subject sci names': 'sscinames',
'subject com names': 'scomnames',
'subject blast names': 'sblastnames',
'subject super kingdoms': 'sskingdoms',
'subject title': 'stitle', 'subject titles': 'salltitles',
'subject strand': 'sstrand',
'% query coverage per subject': 'qcovs',
'% query coverage per hsp': 'qcovhsp',
'Query id': 'qseqid', 'Subject id': 'sseqid',
'gap openings': 'gapopen', 'e-value': 'evalue'}
@blast7.sniffer()
def _blast7_sniffer(fh):
# Smells a BLAST+7 file if the following conditions are present
# -First line contains "BLAST"
# -Second line contains "Query" or "Database"
# -Third line starts with "Subject" or "Query" or "Database"
lines = [line for _, line in zip(range(3), fh)]
if len(lines) < 3:
return False, {}
if not lines[0].startswith("# BLAST"):
return False, {}
if not (lines[1].startswith("# Query:") or
lines[1].startswith("# Database:")):
return False, {}
if not (lines[2].startswith("# Subject:") or
lines[2].startswith("# Query:") or
lines[2].startswith("# Database:")):
return False, {}
return True, {}
@blast7.reader(pd.DataFrame, monkey_patch=False)
def _blast7_to_data_frame(fh):
line_num = 0
columns = None
skiprows = []
for line in fh:
if line == "# Fields: \n":
# Identifies Legacy BLAST 9 data
line = next(fh)
line_num += 1
if columns is None:
columns = _parse_fields(line, legacy=True)
skiprows.append(line_num)
else:
next_columns = _parse_fields(line, legacy=True)
if columns != next_columns:
raise BLAST7FormatError("Fields %r do not equal fields %r"
% (columns, next_columns))
skiprows.append(line_num)
elif line.startswith("# Fields: "):
# Identifies BLAST+7 data
if columns is None:
columns = _parse_fields(line)
else:
# Affirms data types do not differ throught file
next_columns = _parse_fields(line)
if columns != next_columns:
raise BLAST7FormatError("Fields %r do not equal fields %r"
% (columns, next_columns))
line_num += 1
if columns is None:
# Affirms file contains BLAST data
raise BLAST7FormatError("File contains no BLAST data.")
fh.seek(0)
return _parse_blast_data(fh, columns, BLAST7FormatError,
"Number of fields (%r) does not equal number"
" of data columns (%r).", comment='#',
skiprows=skiprows)
def _parse_fields(line, legacy=False):
"""Removes '\n' from fields line and returns fields as a list (columns)."""
line = line.rstrip('\n')
if legacy:
fields = line.split(',')
else:
line = line.split('# Fields: ')[1]
fields = line.split(', ')
columns = []
for field in fields:
if field not in column_converter:
raise BLAST7FormatError("Unrecognized field (%r)."
" Supported fields: %r"
% (field,
set(column_converter.keys())))
columns.append(column_converter[field])
return columns
|
