[Bioperl-l] LocusLink IO

[Paul Boutros]

I think I've extracted a near-minimal set of LL's that give the problem.
The file is about 30 kb, did you want me to zip it and post to group, or
mail direct to you or....

Paul

On Tue, 10 Dec 2002, Hilmar Lapp wrote:

> Paul what would be great if you can compile a sample file with a couple LL entries extracted from your download that trip up the parser and send that to me. Would that be possible? That'd give me something to start from reproducing the error etc.
> 
> 	-hilmar
> 
> > -----Original Message-----
> > From: Paul Boutros [mailto:pcboutro@engmail.uwaterloo.ca]
> > Sent: Tuesday, December 10, 2002 1:00 PM
> > To: bioperl-l@bioperl.org
> > Cc: allenday@ucla.edu
> > Subject: Re: [Bioperl-l] LocusLink IO
> > 
> > 
> > Hi,
> > 
> > I've tried the diff process entirely on a windows box, and 
> > entirely on a
> > Unix box, and there don't appear to be any real differences 
> > between the
> > files.  The ordering of lines in my version (from NCBI) is slightly
> > different than in the test version, and the version I used has some
> > additional information (not *new* tags, just more of the same 
> > ones) than
> > the test one.
> > 
> > But, as best as I can tell, this isn't an \r\n problem -- that was an
> > artifact of me extracting one on a Windows machine and the 
> > other on a Unix
> > server when I did the diff.
> > 
> > I also re-ran my minimal test-case today with a current CVS 
> > tarball, and
> > no changes.  I've also verified it with updated downloads 
> > from NCBI and on
> > a couple of different windows machines.
> > 
> > Any other test I can run to help with this?
> > 
> > Paul
> > 
> > On Tuesday December 3rd You Wrote:
> > 
> > looks like a \r\n problem.  did you happen to untar this file 
> > on a windows
> > or non-os-x-mac box, or do something else with it on one of these
> > platforms?  i got nipped by this problem using winzip to decompress a
> > .tar.gz once.  when i transferred the contents (a bunch of c 
> > source files)  
> > over to a linux box, the compiler had problems reading them b/c the
> > newlines were mangled.
> > 
> > i would try doing the whole decompress/test process on a 
> > linux box, or see
> > if you can find a way to do a binary decompress on the files if you're
> > stuck doing it on old-mac/windows. good luck.
> > 
> > -ad
> > 
> > On Mon, 2 Dec 2002, Paul Boutros wrote:
> > 
> > > I followed the suggestion (I think from Allan Day) of extracting &
> > > diff'ing record 27 from the file.  This is what I got:
> > > 
> > > ===========================
> > > pcboutro@engmail[5] diff testLL.txt LL-sample.seq | more
> > > 43a44
> > > > UNIGENE: Hs.75741
> > > 46d46
> > > < UNIGENE: Hs.75741
> > > 52a53,54
> > > > BUTTON: homol.gif
> > > > LINK:
> > > 
> http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=26[loc]&TAXID
> > =9606
> > 133a136
> > > UNIGENE: Hs.121521
> > 136d138
> > < UNIGENE: Hs.121521
> > 144a147,148
> > > BUTTON: homol.gif
> > > LINK:
> > http://www.ncbi.nlm.nih.gov/HomoloGene/homolquery.cgi?TEXT=27[loc]&TAXID
> > =9606
> > ==========================
> > 
> > The file does indeed terminate with a >> but I didn't see any empty
> lines
> > after that.  I'll submit this as a bug report along with everything I've
> > tested so far.
> > 
> > Paul
> > 
> 
> 
> 
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