[Biopython-dev] [Bug 2740] New: Wise test fails with wise 2.4.1

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2740

           Summary: Wise test fails with wise 2.4.1
           Product: Biopython
           Version: 1.49
          Platform: Other
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: charles-debian-nospam at plessy.org


Dear Biopython developers,

The test for wise fails with wise 2.4.1 and Biopython 1.49. I think one gap is
missing in the reference used in the test script (probably that wise changed
its gap opening penalties):

anx159《Tests》$ dnal Wise/human_114_g01_exons.fna_01
Wise/human_114_g02_exons.fna_01 
Warning Error
        Strangely truncated line in fasta file
Warning Error
        Strangely truncated line in fasta file
DnaAlign Matrix calculation: [  14000] Cells 95%
Score 114
Warning Error
        Name ENSG00000172056|ENST00000321078|ENSE00001281503 is longer than
allowed name block (12). Truncating

Warning Error
        Name ENSG00000163182|ENST00000295339|ENSE00001130648 is longer than
allowed name block (12). Truncating

ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC 
                  A GGAA GCCCC  AGCTC  CT  TCT   CT C TCC    TGC A   TGG  TCC 
ENSG000001631     ATGGAA-GCCCC--AGCTCAGCT--TCT---CTTCCTCC----TGCTACTCTGGC-TCC 


ENSG00000172191   CA                                                          
                  CA                                                          
ENSG0000016347    CA         


This is compared to a different reference result in the test script:

anx159《Tests》$ grep -A5 -B5 ENSG00000172135 test_Wise.py 
        sys.stdout = self.old_stdout

class TestWise(unittest.TestCase):
    def test_align(self):
        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)
        self.assertEqual(temp_file.readline().rstrip(), "ENSG00000172135  
AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC")

def run_tests(argv):
    test_suite = testing_suite()
    runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
    runner.run(test_suite)

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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