[Bioperl-l] LocusLink IO

[Hilmar Lapp]

Send it my way. -hilmar

> -----Original Message-----
> From: Paul Boutros [mailto:pcboutro@engmail.uwaterloo.ca]
> Sent: Tuesday, December 10, 2002 1:55 PM
> To: Hilmar Lapp
> Cc: bioperl-l@bioperl.org; allenday@ucla.edu
> Subject: RE: [Bioperl-l] LocusLink IO
> 
> 
> 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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