[Biopython-dev] [Bug 2740] 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





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-23 07:06 EST -------
Thanks for the report.  Based on the following pages I had assumed the latest
version was wise 2.2.0, available here:

http://www.sanger.ac.uk/Software/Wise2/ points to
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ which only contains up to wise
2.2.0

After some Google searching I found Ewan Birney had changed his mind and stared
work on it again:
http://www.ebi.ac.uk/~birney/wise2/

Installing wise 2.4.1 took a while (tip for Linux uses, edit file
src/models/phasemodel.c line 23 to replace isnumber by isdigit), but I can
confirm the error you reported.

This is the output from an older version of wise,

$ ~/Downloads/wise2.2.0/src/bin/dnal Wise/human_114_g01_exons.fna_01
Wise/human_114_g02_exons.fna_01 
DnaAlign Matrix calculation: [  14000] Cells 97%
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--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC 
                  A GGAA GCCCC  AGCTC  CT  TCT   CT C TCC    TGC A    GG TCCC 
ENSG000001631     ATGGAA-GCCCC--AGCTCAGCT--TCT---CTTCCTCC----TGCTACTCTGGCTCCC 


ENSG00000172192   A                                                           
                  A                                                           
ENSG0000016348    A                                                           


Using the newer version of wise, we do indeed get a different alignment:

$ ~/Downloads/wise2.4.1/src/bin/dnal Wise/human_114_g01_exons.fna_01
Wise/human_114_g02_exons.fna_01 
DnaAlign Matrix calculation: [  14000] Cells 97%
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 


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