# 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 BlastIO parsers."""

import os
import unittest

from Bio.SearchIO import parse
from Bio.SearchIO.BlastIO.blast_tab import _LONG_SHORT_MAP as all_fields

# test case files are in the Blast directory
TEST_DIR = "Blast"
FMT = "blast-tab"


def get_file(filename):
    """Return the path of a test file."""
    return os.path.join(TEST_DIR, filename)


class BlastTabCases(unittest.TestCase):
    """Tests for the tab-separated BLAST parser."""

    def test_tab_2228_tblastn_001(self):
        """Test parsing TBLASTN 2.2.28+ tabular output (tab_2228_tblastn_001)."""
        tab_file = get_file("tab_2228_tblastn_001.txt")
        qresults = list(parse(tab_file, FMT,
                              fields=["evalue", "sallseqid", "qseqid"],
                              comments=True))

        self.assertEqual(1, len(qresults))
        self.assertEqual(10, len(qresults[0].hits))
        # there is one hit with an alternative ID
        self.assertEqual(qresults[0]["gi|148227873|ref|NM_001095167.1|"],
                         qresults[0]["gi|55250552|gb|BC086280.1|"])

        # check some of the HSPs
        self.assertEqual(0.0, qresults[0][0][0].evalue)
        self.assertEqual(8e-173, qresults[0][-1][0].evalue)

    def test_tab_2228_tblastx_001(self):
        """Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001)."""
        tab_file = get_file("tab_2228_tblastx_001.txt")
        qresults = list(parse(tab_file, FMT,
                              fields=list(all_fields.values()),
                              comments=True))

        # this a single query, with 192 hits and 243 hsps
        self.assertEqual(1, len(qresults))
        self.assertEqual(192, len(qresults[0].hits))
        self.assertEqual(243, sum(len(x) for x in qresults[0]))
        # there is one hit with an alternative ID
        self.assertEqual(qresults[0]["gi|31126987|gb|AY255526.2|"],
                         qresults[0]["gi|31342050|ref|NM_181083.2|"])

        # only checking the new fields in 2.2.28+
        hit = qresults[0][0]
        self.assertEqual(["NM_001183135", "EF059095"], hit.accession_all)
        self.assertEqual(["32630", "559292"], hit.tax_ids)
        self.assertEqual(["N/A", "N/A"], hit.sci_names)
        self.assertEqual(["N/A", "N/A"], hit.com_names)
        self.assertEqual(["N/A"], hit.blast_names)
        self.assertEqual(["N/A"], hit.super_kingdoms)
        self.assertEqual("Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", hit.title)
        self.assertEqual(["Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA",
                         "Synthetic construct Saccharomyces cerevisiae clone "
                          "FLH203015.01X MON2, complete sequence"], hit.title_all)
        self.assertEqual("N/A", hit.strand)
        self.assertEqual(100.0, hit.query_coverage)

        for hsp in hit[:4]:
            # shorthand ~ the values just happen to all be 99
            # in other cases, they may be different
            self.assertEqual(99.0, hsp.query_coverage)
        self.assertEqual(73.0, hit[5].query_coverage)
        self.assertEqual(12.0, hit[6].query_coverage)

    def test_tab_2226_tblastn_001(self):
        """Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_001)."""
        xml_file = get_file("tab_2226_tblastn_001.txt")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(34.88, hsp.ident_pct)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(28, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(33.90, hsp.ident_pct)
        self.assertEqual(59, hsp.aln_span)
        self.assertEqual(31, hsp.mismatch_num)
        self.assertEqual(1, hsp.gapopen_num)
        self.assertEqual(43, hsp.query_start)
        self.assertEqual(94, hsp.query_end)
        self.assertEqual(1056, hsp.hit_start)
        self.assertEqual(1233, hsp.hit_end)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)

        # test last qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(95.92, hsp.ident_pct)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(4, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(2e-67, hsp.evalue)
        self.assertEqual(199, hsp.bitscore)

        hsp = hit.hsps[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(29.58, hsp.ident_pct)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(46, hsp.mismatch_num)
        self.assertEqual(2, hsp.gapopen_num)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(4e-05, hsp.evalue)
        self.assertEqual(32.7, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)

    def test_tab_2226_tblastn_002(self):
        """Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_002)."""
        xml_file = get_file("tab_2226_tblastn_002.txt")
        qresults = parse(xml_file, FMT)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)

    def test_tab_2226_tblastn_003(self):
        """Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_003)."""
        xml_file = get_file("tab_2226_tblastn_003.txt")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(34.88, hsp.ident_pct)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(28, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(33.90, hsp.ident_pct)
        self.assertEqual(59, hsp.aln_span)
        self.assertEqual(31, hsp.mismatch_num)
        self.assertEqual(1, hsp.gapopen_num)
        self.assertEqual(43, hsp.query_start)
        self.assertEqual(94, hsp.query_end)
        self.assertEqual(1056, hsp.hit_start)
        self.assertEqual(1233, hsp.hit_end)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_tab_2226_tblastn_004(self):
        """Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_004)."""
        xml_file = get_file("tab_2226_tblastn_004.txt")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(95.92, hsp.ident_pct)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(4, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(2e-67, hsp.evalue)
        self.assertEqual(199, hsp.bitscore)

        hsp = hit.hsps[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(29.58, hsp.ident_pct)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(46, hsp.mismatch_num)
        self.assertEqual(2, hsp.gapopen_num)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(4e-05, hsp.evalue)
        self.assertEqual(32.7, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_tab_2226_tblastn_005(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005)."""
        xml_file = get_file("tab_2226_tblastn_005.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual(0, len(qresult))

        # test second qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(34.88, hsp.ident_pct)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(28, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(33.90, hsp.ident_pct)
        self.assertEqual(59, hsp.aln_span)
        self.assertEqual(31, hsp.mismatch_num)
        self.assertEqual(1, hsp.gapopen_num)
        self.assertEqual(43, hsp.query_start)
        self.assertEqual(94, hsp.query_end)
        self.assertEqual(1056, hsp.hit_start)
        self.assertEqual(1233, hsp.hit_end)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)

        # test last qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(95.92, hsp.ident_pct)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(4, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(2e-67, hsp.evalue)
        self.assertEqual(199, hsp.bitscore)

        hsp = hit.hsps[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(29.58, hsp.ident_pct)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(46, hsp.mismatch_num)
        self.assertEqual(2, hsp.gapopen_num)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(4e-05, hsp.evalue)
        self.assertEqual(32.7, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_tab_2226_tblastn_005_comments_false(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005)."""
        tab_file = get_file("tab_2226_tblastn_005.txt")
        exc_msg = ("Encountered unexpected character '#' at the beginning of"
                   " a line. Set comments=True if the file is a commented"
                   " file.")
        qresults = parse(tab_file, FMT)
        with self.assertRaises(ValueError, msg=exc_msg):
            next(qresults)

    def test_tab_2226_tblastn_006(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_006)."""
        xml_file = get_file("tab_2226_tblastn_006.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual(0, len(qresult))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_tab_2226_tblastn_007(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_007)."""
        xml_file = get_file("tab_2226_tblastn_007.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(34.88, hsp.ident_pct)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(28, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(33.90, hsp.ident_pct)
        self.assertEqual(59, hsp.aln_span)
        self.assertEqual(31, hsp.mismatch_num)
        self.assertEqual(1, hsp.gapopen_num)
        self.assertEqual(43, hsp.query_start)
        self.assertEqual(94, hsp.query_end)
        self.assertEqual(1056, hsp.hit_start)
        self.assertEqual(1233, hsp.hit_end)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_tab_2226_tblastn_008(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_008)."""
        xml_file = get_file("tab_2226_tblastn_008.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(95.92, hsp.ident_pct)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(4, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(2e-67, hsp.evalue)
        self.assertEqual(199, hsp.bitscore)

        hsp = hit.hsps[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(29.58, hsp.ident_pct)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(46, hsp.mismatch_num)
        self.assertEqual(2, hsp.gapopen_num)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(4e-05, hsp.evalue)
        self.assertEqual(32.7, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_tab_2226_tblastn_009(self):
        """Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_009)."""
        xml_file = get_file("tab_2226_tblastn_009.txt")
        qresults = parse(xml_file, FMT, fields=("qseqid", "sseqid"))
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("<unknown program>", qresult.program)
        self.assertEqual("<unknown target>", qresult.target)
        self.assertEqual("<unknown version>", qresult.version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)

        # test last qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("<unknown program>", qresult.program)
        self.assertEqual("<unknown target>", qresult.target)
        self.assertEqual("<unknown version>", qresult.version)
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(2, len(hit))

        hsp = hit[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)

        hsp = hit[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)

    def test_tab_2226_tblastn_010(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_010)."""
        xml_file = get_file("tab_2226_tblastn_010.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual(0, len(qresult))

        # test second qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)

        # test last qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(2e-67, hsp.evalue)
        self.assertEqual(199, hsp.bitscore)

        hsp = hit.hsps[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(4e-05, hsp.evalue)
        self.assertEqual(32.7, hsp.bitscore)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_tab_2226_tblastn_011(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_011)."""
        xml_file = get_file("tab_2226_tblastn_011.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual(0, len(qresult))

        # test second qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.accession)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.accession_version)
        self.assertEqual("0", qresult.gi)
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual(["gi|145479850|ref|XM_001425911.1|"], hit.id_all)
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.accession)
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.accession_version)
        self.assertEqual("0", hit.gi)
        self.assertEqual("0", hit.gi_all)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(4632, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(34.88, hsp.ident_pct)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(28, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)
        self.assertEqual("PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD", str(hsp.query.seq))
        self.assertEqual("PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID", str(hsp.hit.seq))
        self.assertEqual(78, hsp.bitscore_raw)
        self.assertEqual(15, hsp.ident_num)
        self.assertEqual(26, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(60.47, hsp.pos_pct)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.accession)
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.accession_version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(33.90, hsp.ident_pct)
        self.assertEqual(59, hsp.aln_span)
        self.assertEqual(31, hsp.mismatch_num)
        self.assertEqual(1, hsp.gapopen_num)
        self.assertEqual(43, hsp.query_start)
        self.assertEqual(94, hsp.query_end)
        self.assertEqual(1056, hsp.hit_start)
        self.assertEqual(1233, hsp.hit_end)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)
        self.assertEqual("GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL", str(hsp.query.seq))
        self.assertEqual("GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", str(hsp.hit.seq))
        self.assertEqual(70.0, hsp.bitscore_raw)
        self.assertEqual(20, hsp.ident_num)
        self.assertEqual(29, hsp.pos_num)
        self.assertEqual(8, hsp.gap_num)
        self.assertEqual(49.15, hsp.pos_pct)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)

        # test last qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("gi|11464971:4-101", qresult.accession)
        self.assertEqual("gi|11464971:4-101", qresult.accession_version)
        self.assertEqual("0", qresult.gi)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual(["gi|350596019|ref|XM_003360601.2|"], hit.id_all)
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.accession)
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.accession_version)
        self.assertEqual("0", hit.gi)
        self.assertEqual("0", hit.gi_all)
        self.assertEqual("gi|11464971:4-101", hit.query_id)
        self.assertEqual(772, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(95.92, hsp.ident_pct)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(4, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(2e-67, hsp.evalue)
        self.assertEqual(199, hsp.bitscore)
        self.assertEqual("KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", str(hsp.query.seq))
        self.assertEqual("KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK", str(hsp.hit.seq))
        self.assertEqual(506.0, hsp.bitscore_raw)
        self.assertEqual(94, hsp.ident_num)
        self.assertEqual(96, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(97.96, hsp.pos_pct)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)

        hsp = hit.hsps[-1]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hsp.hit_id)
        self.assertEqual("gi|11464971:4-101", hsp.query_id)
        self.assertEqual(29.58, hsp.ident_pct)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(46, hsp.mismatch_num)
        self.assertEqual(2, hsp.gapopen_num)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(4e-05, hsp.evalue)
        self.assertEqual(32.7, hsp.bitscore)
        self.assertEqual("IEFYKKKSDNSPKGMIPLKGSTLTS-PCQDFGKRMFVLK---ITTTKQQDHFFQAAFLEERDAWVRDIKKA", str(hsp.query.seq))
        self.assertEqual("LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKERTEWIKAIQVA", str(hsp.hit.seq))
        self.assertEqual(73.0, hsp.bitscore_raw)
        self.assertEqual(21, hsp.ident_num)
        self.assertEqual(33, hsp.pos_num)
        self.assertEqual(4, hsp.gap_num)
        self.assertEqual(46.48, hsp.pos_pct)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_tab_2226_tblastn_012(self):
        """Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_012)."""
        xml_file = get_file("tab_2226_tblastn_012.txt")
        qresults = parse(xml_file, FMT, comments=True)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("refseq_rna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("X76FDCG9016", qresult.rid)
        self.assertEqual(0, len(qresult))

        # test second qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("refseq_rna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual("X76FDCG9016", qresult.rid)
        self.assertEqual(3, len(qresult))

        # test last qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("refseq_rna", qresult.target)
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("X76FDCG9016", qresult.rid)
        self.assertEqual(5, len(qresult))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_tab_2226_tblastn_013(self):
        """Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_013)."""
        xml_file = get_file("tab_2226_tblastn_013.txt")
        qresults = parse(xml_file, FMT, fields="qseq std sseq")
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("<unknown program>", qresult.program)
        self.assertEqual("<unknown target>", qresult.target)
        self.assertEqual("<unknown version>", qresult.version)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(34.88, hsp.ident_pct)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(28, hsp.mismatch_num)
        self.assertEqual(0, hsp.gapopen_num)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(1e-05, hsp.evalue)
        self.assertEqual(34.7, hsp.bitscore)
        self.assertEqual("PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD", str(hsp.query.seq))
        self.assertEqual("PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID", str(hsp.hit.seq))

        hit = qresult[-1]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hit.id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.query_id)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual("gi|115975252|ref|XM_001180111.1|", hsp.hit_id)
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hsp.query_id)
        self.assertEqual(33.90, hsp.ident_pct)
        self.assertEqual(59, hsp.aln_span)
        self.assertEqual(31, hsp.mismatch_num)
        self.assertEqual(1, hsp.gapopen_num)
        self.assertEqual(43, hsp.query_start)
        self.assertEqual(94, hsp.query_end)
        self.assertEqual(1056, hsp.hit_start)
        self.assertEqual(1233, hsp.hit_end)
        self.assertEqual(1e-04, hsp.evalue)
        self.assertEqual(31.6, hsp.bitscore)
        self.assertEqual("GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL", str(hsp.query.seq))
        self.assertEqual("GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", str(hsp.hit.seq))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)


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