"""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**

+------+------+---------------------------------------------------------------+
|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      |sskingdoms            |
|kingdoms           |                      |
+-------------------+----------------------+
|subject title      |stitle                |
+-------------------+----------------------+
|subject strand     |sstrand               |
+-------------------+----------------------+
|subject titles     |salltitles            |
+-------------------+----------------------+
|% query coverage   |qcovs                 |
|per subject        |                      |
+-------------------+----------------------+
|% query coverage   |qcovhsp               |
|per 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[['qseqid', 'sseqid', 'pident']] # doctest: +NORMALIZE_WHITESPACE
     qseqid          sseqid  pident
0  AF178033  EMORG:AF178033  100.00
1  AF178033  EMORG:AF178032   94.57
2  AF178033  EMORG:AF178031   94.82

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/


"""  # noqa: D205, D415

# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.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):
    r"""Remove '\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