# Copyright 2012 by Wibowo Arindrarto.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Tests for SearchIO blast-tab indexing."""

import unittest

from search_tests_common import CheckRaw, CheckIndex


class BlastTabRawCases(CheckRaw):
    """Check BLAST tabular get_raw method."""

    fmt = 'blast-tab'

    def test_blasttab_2226_multiple_first(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first (tab_2226_tblastn_001.txt)"""
        filename = 'Blast/tab_2226_tblastn_001.txt'
        raw = """gi|16080617|ref|NP_391444.1|	gi|145479850|ref|XM_001425911.1|	34.88	43	28	0	31	73	1744	1872	1e-05	34.7
gi|16080617|ref|NP_391444.1|	gi|72012412|ref|XM_777959.1|	33.90	59	31	1	44	94	1057	1233	1e-04	31.6
gi|16080617|ref|NP_391444.1|	gi|115975252|ref|XM_001180111.1|	33.90	59	31	1	44	94	1057	1233	1e-04	31.6
"""
        self.check_raw(filename, "gi|16080617|ref|NP_391444.1|", raw)

    def test_blasttab_2226_multiple_last(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last (tab_2226_tblastn_001.txt)"""
        filename = 'Blast/tab_2226_tblastn_001.txt'
        raw = """gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	95.92	98	4	0	1	98	95	388	2e-67	 199
gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	29.58	71	46	2	30	96	542	754	4e-05	32.7
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	97.96	98	2	0	1	98	78	371	2e-67	 202
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	30.00	100	64	2	3	96	804	1103	3e-09	45.1
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	97.96	98	2	0	1	98	161	454	4e-67	 202
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	30.00	100	64	2	3	96	866	1165	3e-09	45.1
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	97.96	98	2	0	1	98	173	466	2e-66	 202
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	31.00	100	63	2	3	96	899	1198	1e-09	46.6
gi|11464971:4-101	gi|365982352|ref|XM_003667962.1|	30.77	52	27	1	12	54	3181	3336	1.7	19.6
"""
        self.check_raw(filename, "gi|11464971:4-101", raw)

    def test_blasttab_2226_single(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt)"""
        filename = 'Blast/tab_2226_tblastn_004.txt'
        raw = """gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	95.92	98	4	0	1	98	95	388	2e-67	 199
gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	29.58	71	46	2	30	96	542	754	4e-05	32.7
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	97.96	98	2	0	1	98	78	371	2e-67	 202
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	30.00	100	64	2	3	96	804	1103	3e-09	45.1
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	97.96	98	2	0	1	98	161	454	4e-67	 202
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	30.00	100	64	2	3	96	866	1165	3e-09	45.1
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	97.96	98	2	0	1	98	173	466	2e-66	 202
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	31.00	100	63	2	3	96	899	1198	1e-09	46.6
gi|11464971:4-101	gi|365982352|ref|XM_003667962.1|	30.77	52	27	1	12	54	3181	3336	1.7	19.6
"""
        self.check_raw(filename, "gi|11464971:4-101", raw)

    def test_blasttab_2226_multiple_first_commented(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first, commented (tab_2226_tblastn_005.txt)"""
        filename = 'Blast/tab_2226_tblastn_005.txt'
        raw = """# TBLASTN 2.2.26+
# Query: random_s00
# Database: db/minirefseq_mrna
# 0 hits found
"""
        self.check_raw(filename, "random_s00", raw, comments=True)

    def test_blasttab_2226_multiple_middle_commented(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, middle, commented (tab_2226_tblastn_005.txt)"""
        filename = 'Blast/tab_2226_tblastn_005.txt'
        raw = """# TBLASTN 2.2.26+
# Query: gi|16080617|ref|NP_391444.1| membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]
# Database: db/minirefseq_mrna
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 3 hits found
gi|16080617|ref|NP_391444.1|	gi|145479850|ref|XM_001425911.1|	34.88	43	28	0	31	73	1744	1872	1e-05	34.7
gi|16080617|ref|NP_391444.1|	gi|72012412|ref|XM_777959.1|	33.90	59	31	1	44	94	1057	1233	1e-04	31.6
gi|16080617|ref|NP_391444.1|	gi|115975252|ref|XM_001180111.1|	33.90	59	31	1	44	94	1057	1233	1e-04	31.6
"""
        self.check_raw(filename, "gi|16080617|ref|NP_391444.1|", raw, comments=True)

    def test_blasttab_2226_multiple_last_commented(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last, commented (tab_2226_tblastn_005.txt)"""
        filename = 'Blast/tab_2226_tblastn_005.txt'
        raw = """# TBLASTN 2.2.26+
# Query: gi|11464971:4-101 pleckstrin [Mus musculus]
# Database: db/minirefseq_mrna
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 9 hits found
gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	95.92	98	4	0	1	98	95	388	2e-67	 199
gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	29.58	71	46	2	30	96	542	754	4e-05	32.7
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	97.96	98	2	0	1	98	78	371	2e-67	 202
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	30.00	100	64	2	3	96	804	1103	3e-09	45.1
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	97.96	98	2	0	1	98	161	454	4e-67	 202
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	30.00	100	64	2	3	96	866	1165	3e-09	45.1
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	97.96	98	2	0	1	98	173	466	2e-66	 202
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	31.00	100	63	2	3	96	899	1198	1e-09	46.6
gi|11464971:4-101	gi|365982352|ref|XM_003667962.1|	30.77	52	27	1	12	54	3181	3336	1.7	19.6
"""
        self.check_raw(filename, "gi|11464971:4-101", raw, comments=True)

    def test_blasttab_2226_single_commented(self):
        """Test blast-tab raw string retrieval, BLAST 2.2.26+, single query, commented (tab_2226_tblastn_008.txt)"""
        filename = 'Blast/tab_2226_tblastn_008.txt'
        raw = """# TBLASTN 2.2.26+
# Query: gi|11464971:4-101 pleckstrin [Mus musculus]
# Database: db/minirefseq_mrna
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 9 hits found
gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	95.92	98	4	0	1	98	95	388	2e-67	 199
gi|11464971:4-101	gi|350596019|ref|XM_003360601.2|	29.58	71	46	2	30	96	542	754	4e-05	32.7
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	97.96	98	2	0	1	98	78	371	2e-67	 202
gi|11464971:4-101	gi|301779869|ref|XM_002925302.1|	30.00	100	64	2	3	96	804	1103	3e-09	45.1
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	97.96	98	2	0	1	98	161	454	4e-67	 202
gi|11464971:4-101	gi|296223671|ref|XM_002757683.1|	30.00	100	64	2	3	96	866	1165	3e-09	45.1
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	97.96	98	2	0	1	98	173	466	2e-66	 202
gi|11464971:4-101	gi|338714227|ref|XM_001492113.3|	31.00	100	63	2	3	96	899	1198	1e-09	46.6
gi|11464971:4-101	gi|365982352|ref|XM_003667962.1|	30.77	52	27	1	12	54	3181	3336	1.7	19.6
"""
        self.check_raw(filename, "gi|11464971:4-101", raw, comments=True)


class BlastTabIndexCases(CheckIndex):

    fmt = 'blast-tab'

    def test_blasttab_2226_tblastn_001(self):
        """Test blast-tab indexing, BLAST 2.2.26+, multiple queries"""
        filename = 'Blast/tab_2226_tblastn_001.txt'
        self.check_index(filename, self.fmt)

    def test_blasttab_2226_tblastn_002(self):
        """Test blast-tab indexing, BLAST 2.2.26+, single query, no hits"""
        filename = 'Blast/tab_2226_tblastn_002.txt'
        self.check_index(filename, self.fmt)

    def test_blasttab_2226_tblastn_004(self):
        """Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits"""
        filename = 'Blast/tab_2226_tblastn_004.txt'
        self.check_index(filename, self.fmt)

    def test_blasttab_2226_tblastn_005(self):
        """Test blast-tab indexing, BLAST 2.2.26+, multiple queries, commented"""
        filename = 'Blast/tab_2226_tblastn_005.txt'
        self.check_index(filename, self.fmt, comments=True)

    def test_blasttab_2226_tblastn_006(self):
        """Test blast-tab indexing, BLAST 2.2.26+, single query, no hits, commented"""
        filename = 'Blast/tab_2226_tblastn_006.txt'
        self.check_index(filename, self.fmt, comments=True)

    def test_blasttab_comment_sing(self):
        """Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits, commented"""
        filename = 'Blast/tab_2226_tblastn_008.txt'
        self.check_index(filename, self.fmt, comments=True)

    def test_blasttab_2226_tblastn_009(self):
        """Test blast-tab indexing, BLAST 2.2.26+, custom columns"""
        filename = 'Blast/tab_2226_tblastn_009.txt'
        self.check_index(filename, self.fmt, fields=['qseqid', 'sseqid'])

    def test_blasttab_2226_tblastn_010(self):
        """Test blast-tab indexing, BLAST 2.2.26+, custom columns, commented"""
        filename = 'Blast/tab_2226_tblastn_010.txt'
        self.check_index(filename, self.fmt, comments=True)

    def test_blasttab_2226_tblastn_011(self):
        """Test blast-tab indexing, BLAST 2.2.26+, all columns, commented"""
        filename = 'Blast/tab_2226_tblastn_011.txt'
        self.check_index(filename, self.fmt, comments=True)


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)