[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 20:21:12 EST 2008


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


mukhyala at gene.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #18 from mukhyala at gene.com  2008-11-18 20:21 EST -------
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

you can reproduce this using the following sequence :
>Unison:8209920
MGTAAAAAAAGEGARGPSPAAVSLGLGVAVVSSLVNGSTFVLQKKGIVRAKRRGTSYLTD
IVWWAGTIAMAVGQIGNFLAYTAVPTVLVTPLGALGVPFGSILASYLLKEKLNILGKLGC
LLSCAGSVVLIIHSPKSESVTSQAELEEKLTNPVFVGYLCIVLLMLLLLIFWIAPAHGPT
NIMVYISICSLLGSFTVPSTKGIGLAAQDILHNNPSSQRALCLCLVLLAVLGCSIIVQFR
YINKALECFDSSVFGAIYYVVFTTLVLLASAILFREWSNVGLVDFLGMACGFTTVSVGIV
LIQVFKEFNFNLGEMNKSNMKTD

and the pfam 23.0 model for PF09721.2.



(In reply to comment #16)
> The verbose flag was set; the 'Something's wrong at...' is from undefined or
> empty strings being passed along via debug() to CORE::warn.  I turned off
> verbose but went ahead and removed the debugging lines as well (leftovers from
> the bug fix I forgot to take out).
> 


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