[Bioperl-l] Issue with Bio::SearchIO::psl (was: Bioperl bug 1977)

Albert Vernon Smith smithav at cshl.edu
Tue Apr 4 11:15:42 EDT 2006


I deleted all of my bioperl installation, and reinstalled to be  
certain that this is a current issue.  Having done that, I am still  
seeing the issue.  I also updated IO::Handle to the most recent  
version, on the off chance that it was something coming from there.

-albert


On 1.4.2006, at 06:54, Chris Fields wrote:

> Albert,
>
> I had no problems with this on Mac OS X (I'm running from 10.4.5,  
> perl 5.8.6).  I noticed that several fixes were made in the last 6  
> months that would potentially fix this issue, including two which  
> involve newlines (that is what seems to be hanging things up  
> here).  Have you tried a full bioperl-live install to see if that  
> fixes it?
>
> computer:~/searchio_test cjfields$ perl psl.pl
> /usr/local/blat/db/hg17/hg17.2bit:chr5
>     100.00
> /usr/local/blat/db/hg17/hg17.2bit:chr21
>     90.00
> /usr/local/blat/db/hg17/hg17.2bit:chr5
>     85.00
> /usr/local/blat/db/hg17/hg17.2bit:chr13
>     80.00
> /usr/local/blat/db/hg17/hg17.2bit:chr7
>     80.00
>
>
> Chris



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