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"""
BLAST+6 format (:mod:`skbio.io.format.blast6`)
==============================================
.. currentmodule:: skbio.io.format.blast6
The BLAST+6 format (``blast+6``) stores the results of a BLAST [1]_ database
search. The results are stored in a simple tabular format with no column
headers. Values are separated by the tab character.
An example BLAST+6-formatted file comparing two protein sequences, taken
from [2]_ (tab characters represented by ``<tab>``)::
moaC<tab>gi|15800534|ref|NP_286546.1|<tab>100.00<tab>161<tab>0<tab>0<tab>1\
<tab>161<tab>1<tab>161<tab>3e-114<tab>330
moaC<tab>gi|170768970|ref|ZP_02903423.1|<tab>99.38<tab>161<tab>1<tab>0\
<tab>1<tab>161<tab>1<tab>161<tab>9e-114<tab>329
Format Support
--------------
**Has Sniffer: No**
**State: Experimental as of 0.4.1.**
+------+------+---------------------------------------------------------------+
|Reader|Writer| Object Class |
+======+======+===============================================================+
|Yes |No |:mod:`pandas.DataFrame` |
+------+------+---------------------------------------------------------------+
Format Specification
--------------------
BLAST+6 format is a tabular text-based format produced by both BLAST+ output
format 6 (``-outfmt 6``) and legacy BLAST output format 8 (``-m 8``). It is
tab-separated and has no column headers. With BLAST+, users can specify the
columns that are present in their BLAST output file by specifying column names
(e.g., ``-outfmt "6 qseqid sseqid bitscore qstart sstart"``), if the default
columns output by BLAST are not desired.
BLAST Column Types
^^^^^^^^^^^^^^^^^^
The following column types are output by BLAST and supported by scikit-bio.
This information is taken from [3]_.
+-----------+------------------------------------+-----+
|Name |Description |Type |
+===========+====================================+=====+
|qseqid |Query Seq-id |str |
+-----------+------------------------------------+-----+
|qgi |Query GI |int |
+-----------+------------------------------------+-----+
|qacc |Query accesion |str |
+-----------+------------------------------------+-----+
|qaccver |Query accesion.version |str |
+-----------+------------------------------------+-----+
|qlen |Query sequence length |int |
+-----------+------------------------------------+-----+
|sseqid |Subject Seq-id |str |
+-----------+------------------------------------+-----+
|sallseqid |All subject Seq-id(s), separated by |str |
| |a ';' | |
+-----------+------------------------------------+-----+
|sgi |Subject GI |int |
+-----------+------------------------------------+-----+
|sallgi |All subject GIs |int |
+-----------+------------------------------------+-----+
|sacc |Subject accesion |str |
+-----------+------------------------------------+-----+
|saccver |Subject accesion.version |str |
+-----------+------------------------------------+-----+
|sallacc |All subject accesions |str |
+-----------+------------------------------------+-----+
|slen |Subject sequence length |int |
+-----------+------------------------------------+-----+
|qstart |Start of alignment in query |int |
+-----------+------------------------------------+-----+
|qend |End of alignment in query |int |
+-----------+------------------------------------+-----+
|sstart |Start of alignment in subject |int |
+-----------+------------------------------------+-----+
|send |End of alignment in subject |int |
+-----------+------------------------------------+-----+
|qseq |Aligned part of query sequence |str |
+-----------+------------------------------------+-----+
|sseq |Aligned part of subject sequence |str |
+-----------+------------------------------------+-----+
|evalue |Expect value |float|
+-----------+------------------------------------+-----+
|bitscore |Bit score |float|
+-----------+------------------------------------+-----+
|score |Raw score |int |
+-----------+------------------------------------+-----+
|length |Alignment length |int |
+-----------+------------------------------------+-----+
|pident |Percent of identical matches |float|
+-----------+------------------------------------+-----+
|nident |Number of identical matches |int |
+-----------+------------------------------------+-----+
|mismatch |Number of mismatches |int |
+-----------+------------------------------------+-----+
|positive |Number of positive-scoring matches |int |
+-----------+------------------------------------+-----+
|gapopen |Number of gap openings |int |
+-----------+------------------------------------+-----+
|gaps |Total number of gaps |int |
+-----------+------------------------------------+-----+
|ppos |Percentage of positive-scoring matc\|float|
| |hes | |
+-----------+------------------------------------+-----+
|frames |Query and subject frames separated |str |
| |by a '/' | |
+-----------+------------------------------------+-----+
|qframe |Query frame |int |
+-----------+------------------------------------+-----+
|sframe |Subject frame |int |
+-----------+------------------------------------+-----+
|btop |Blast traceback operations (BTOP) |int |
+-----------+------------------------------------+-----+
|staxids |Unique Subject Taxonomy ID(s), sepa\|str |
| |rated by a ';' (in numerical order) | |
+-----------+------------------------------------+-----+
|sscinames |Unique Subject Scientific Name(s), |str |
| |separated by a ';' | |
+-----------+------------------------------------+-----+
|scomnames |Unique Subject Common Name(s), sepa\|str |
| |rated by a ';' | |
+-----------+------------------------------------+-----+
|sblastnames|unique Subject Blast Name(s), separ\|str |
| |ated by a ';' (in alphabetical | |
| |order) | |
+-----------+------------------------------------+-----+
|sskingdoms |unique Subject Super Kingdom(s), se\|str |
| |parated by a ';' (in alphabetical | |
| |order) | |
+-----------+------------------------------------+-----+
|stitle |Subject Title |str |
+-----------+------------------------------------+-----+
|sstrand |Subject Strand |str |
+-----------+------------------------------------+-----+
|salltitles |All Subject Title(s), separated by |str |
| |a '<>' | |
+-----------+------------------------------------+-----+
|qcovs |Query Coverage Per Subject |int |
+-----------+------------------------------------+-----+
|qcovhsp |Query Coverage Per HSP |int |
+-----------+------------------------------------+-----+
.. note:: When a BLAST+6-formatted file contains ``N/A`` values, scikit-bio
will convert these values into ``np.nan``, matching pandas' convention for
representing missing data.
.. note:: scikit-bio stores columns of type ``int`` as type ``float`` in the
returned ``pd.DataFrame``. This is necessary in order to allow ``N/A``
values in integer columns (this is currently a limitation of pandas).
Format Parameters
-----------------
The following format parameters are available in ``blast+6`` format:
- ``default_columns``: ``False`` by default. If ``True``, will use the default
columns output by BLAST, which are qseqid, sseqid, pident, length, mismatch,
gapopen, qstart, qend, sstart, send, evalue, and bitscore.
.. warning:: When reading legacy BLAST files, you must pass
``default_columns=True`` because legacy BLAST does not allow users to
specify which columns are present in the output file.
- ``columns``: ``None`` by default. If provided, must be a list of column names
in the order they will appear in the file.
.. note:: Either ``default_columns`` or ``columns`` must be provided, as
``blast+6`` does not contain column headers.
Examples
--------
Suppose we have a ``blast+6`` file with default columns:
>>> from io import StringIO
>>> import skbio.io
>>> import pandas as pd
>>> fs = '\\n'.join([
... 'moaC\\tgi|15800534|ref|NP_286546.1|\\t100.00\\t161\\t0\\t0\\t1\\t161\
\\t1\\t161\\t3e-114\\t330',
... 'moaC\\tgi|170768970|ref|ZP_02903423.1|\\t99.38\\t161\\t1\\t0\\t1\\t\
161\\t1\\t161\\t9e-114\\t329'
... ])
>>> fh = StringIO(fs)
Read the file into a ``pd.DataFrame`` and specify that default columns should
be used:
>>> df = skbio.io.read(fh, format="blast+6", into=pd.DataFrame,
... default_columns=True)
>>> df # doctest: +NORMALIZE_WHITESPACE
qseqid sseqid pident length mismatch gapopen \\
0 moaC gi|15800534|ref|NP_286546.1| 100.00 161.0 0.0 0.0
1 moaC gi|170768970|ref|ZP_02903423.1| 99.38 161.0 1.0 0.0
<BLANKLINE>
qstart qend sstart send evalue bitscore
0 1.0 161.0 1.0 161.0 3.000000e-114 330.0
1 1.0 161.0 1.0 161.0 9.000000e-114 329.0
Suppose we have a ``blast+6`` file with user-supplied (non-default) columns:
>>> from io import StringIO
>>> import skbio.io
>>> import pandas as pd
>>> fs = '\\n'.join([
... 'moaC\\t100.00\\t0\\t161\\t0\\t161\\t330\\t1',
... 'moaC\\t99.38\\t1\\t161\\t0\\t161\\t329\\t1'
... ])
>>> fh = StringIO(fs)
Read the file into a ``pd.DataFrame`` and specify which columns are present
in the file:
>>> df = skbio.io.read(fh, format="blast+6", into=pd.DataFrame,
... columns=['qseqid', 'pident', 'mismatch', 'length',
... 'gapopen', 'qend', 'bitscore', 'sstart'])
>>> df # doctest: +NORMALIZE_WHITESPACE
qseqid pident mismatch length gapopen qend bitscore sstart
0 moaC 100.00 0.0 161.0 0.0 161.0 330.0 1.0
1 moaC 99.38 1.0 161.0 0.0 161.0 329.0 1.0
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://blastedbio.blogspot.com/2014/11/column-headers-in-blast-tabular-\
and-csv.html
.. [3] http://www.ncbi.nlm.nih.gov/books/NBK279675/
"""
# ----------------------------------------------------------------------------
# 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
from skbio.io.format._blast import _parse_blast_data, _possible_columns
blast6 = create_format('blast+6')
_default_columns = ['qseqid', 'sseqid', 'pident', 'length', 'mismatch',
'gapopen', 'qstart', 'qend', 'sstart', 'send',
'evalue', 'bitscore']
@blast6.reader(pd.DataFrame, monkey_patch=False)
def _blast6_to_data_frame(fh, columns=None, default_columns=False):
if default_columns and columns is not None:
raise ValueError("`columns` and `default_columns` cannot both be"
" provided.")
if not default_columns and columns is None:
raise ValueError("Either `columns` or `default_columns` must be"
" provided.")
if default_columns:
columns = _default_columns
else:
for column in columns:
if column not in _possible_columns:
raise ValueError("Unrecognized column (%r)."
" Supported columns:\n%r" %
(column, set(_possible_columns.keys())))
return _parse_blast_data(fh, columns, ValueError,
"Specified number of columns (%r) does not equal"
" number of columns in file (%r).")
|
