[Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Nov 18 22:01:16 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2632





------- Comment #19 from cjfields at bioperl.org  2008-11-18 22:01 EST -------
Can you attach an example report for this?  That would be greatly appreciated. 

I can't debug on my local machine w/o installing/running HMMER against Pfam
(and I don't have time to do that at this moment).

(In reply to comment #18)
> The fix doesn't work for cases where the match line in the alignment block
> starts with a " CS ". See below:
> 
>                    ACSGlrsLiallalgllyayl...frrslwrrllllllaiipiailaNvl
>                     CS l+s+    + g  +a+ +  +  ++ +r+l+l+  + ++a+l+
>   Unison:820   189 -CSLLGSFTVPSTKGIGLAAQdilHNNPSSQRALCLC-LV-LLAVLG--- 232
> ....


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