Example #1
0
 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)
     self.assert_(sys.stdout.getvalue().startswith(
         "dnal -kbyte 100000 seq1.fna seq2.fna"))
Example #2
0
 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)
     #If test output is redirected to a file, the wrapper adds -quiet
     output = sys.stdout.getvalue().replace(" -quiet ", " ")
     self.assertTrue(output.startswith("psw -kbyte 4 seq1.faa seq2.faa"),
                     output[:200])
Example #3
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 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])
Example #4
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 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":
         # Wise 2.4.1 includes a score line, even in quiet mode, ignore this
         line = temp_file.readline().rstrip()
     if (line ==
             "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC"
         ):
         # This is what we expect from wise 2.2.0 (and earlier)
         pass
     elif (line ==
           "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC"
           ):
         # This is what we expect from wise 2.4.1
         pass
     else:
         # Bad!
         self.fail(line)
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)
    except AttributeError:
        try:
            keywds['dry_run']
            return None
        except KeyError:
            raise
Example #6
0
def align(pair, scores=None, gap_start=None, gap_extension=None, *args, **keywds):

    cmdline = _CMDLINE_PSW[:]
    if scores:
        cmdline.extend((_OPTION_SCORES, scores))
    if gap_start:
        cmdline.extend((_OPTION_GAP_START, str(gap_start)))
    if gap_extension:
        cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
    temp_file = Wise.align(cmdline, pair, *args, **keywds)
    return parse(temp_file)
Example #7
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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)
    except AttributeError:
        try:
            keywds['dry_run']
            return None
        except KeyError:
            raise
Example #8
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def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
    """Align a pair of DNA files using dnal and calculate the statistics of the alignment."""
    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)
    except AttributeError:
        try:
            keywds['dry_run']
            return None
        except KeyError:
            raise
Example #9
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def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
    """Align a pair of DNA files using dnal and calculate the statistics of the alignment."""
    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)
    except AttributeError:
        try:
            keywds['dry_run']
            return None
        except KeyError:
            raise
Example #10
0
def align(pair,
          scores=None,
          gap_start=None,
          gap_extension=None,
          *args, **keywds):
    cmdline = _CMDLINE_PSW[:]
    if scores:
        cmdline.extend((_OPTION_SCORES, scores))
    if gap_start:
        cmdline.extend((_OPTION_GAP_START, str(gap_start)))
    if gap_extension:
        cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
    temp_file = Wise.align(cmdline, pair, *args, **keywds)
    return parse(temp_file)
Example #11
0
 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" :
         #Wise 2.4.1 includes a score line, even in quiet mode, ignore this
         line = temp_file.readline().rstrip()
     if line == "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC" :
         #This is what we expect from wise 2.2.0 (and earlier)
         pass
     elif line == "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC" :
         #This is what we expect from wise 2.4.1
         pass
     else :
         #Bad!
         self.assert_(False, line)
Example #12
0
 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)
     self.assert_(sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))
Example #13
0
 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)
     self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000 seq1.fna seq2.fna"))
Example #14
0
 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)
     # If test output is redirected to a file, the wrapper adds -quiet
     output = sys.stdout.getvalue().replace(" -quiet ", " ")
     self.assertTrue(output.startswith("psw -kbyte 4 seq1.faa seq2.faa"), output[:200])
Example #15
0
 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])
Example #16
0
 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)
     self.assert_(
         sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))