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src/b/i/biopython-1.63/Bio/Wise/psw.py   biopython(Download)
    if gap_extension:
        cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
    temp_file = Wise.align(cmdline, pair, *args, **keywds)
    return parse(temp_file)
 

src/b/i/biopython-1.63/Bio/Wise/dnal.py   biopython(Download)
def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
    cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
    temp_file = Wise.align(cmdline, pair, **keywds)
    try:
        return Statistics(temp_file.name, match, mismatch, gap, extension)

src/b/i/biopython-HEAD/Bio/Wise/psw.py   biopython(Download)
    if gap_extension:
        cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
    temp_file = Wise.align(cmdline, pair, *args, **keywds)
    return parse(temp_file)
 

src/b/i/biopython-HEAD/Bio/Wise/dnal.py   biopython(Download)
def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
    cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
    temp_file = Wise.align(cmdline, pair, **keywds)
    try:
        return Statistics(temp_file.name, match, mismatch, gap, extension)

src/b/i/biopython-1.63/Tests/test_Wise.py   biopython(Download)
    def test_dnal(self):
        """Call dnal, and do a trivial check on its output."""
        Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
        #If test output is redirected to a file, the wrapper adds -quiet
        output = sys.stdout.getvalue().replace(" -quiet ", " ")
        self.assertTrue(output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"), output[:200])
 
    def test_psw(self):
        """Call psw, and do a trivial check on its output."""
        Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
    def test_align(self):
        """Call dnal with optional arguments, and do a trivial check on the output."""
        temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
        line = temp_file.readline().rstrip()
        if line == "Score 114":

src/b/i/biopython-HEAD/Tests/test_Wise.py   biopython(Download)
    def test_dnal(self):
        """Call dnal, and do a trivial check on its output."""
        Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
        #If test output is redirected to a file, the wrapper adds -quiet
        output = sys.stdout.getvalue().replace(" -quiet ", " ")
        self.assertTrue(output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"), output[:200])
 
    def test_psw(self):
        """Call psw, and do a trivial check on its output."""
        Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
    def test_align(self):
        """Call dnal with optional arguments, and do a trivial check on the output."""
        temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
        line = temp_file.readline().rstrip()
        if line == "Score 114":