[Bioperl-l] Linefeed mix-up (bug #903)

[Jason Stajich]

On Thu, 22 Feb 2001, Ewan Birney wrote:

> On Thu, 22 Feb 2001, Brad Langhorst wrote:
> 
> > On Thursday 22 February 2001 02:46 am, you wrote:
> > > "Brad Langohrst (by way of Brad Langohrst )" wrote:
> > > > I've been a lurker for a really long while....
> > > >
> > > > It should be possible to do the parse without passing any extra
> > > > parameters. If you know the file you are reading is a relatively small
> > > > text file this method should be safe to use...
> > > >
> > > > 1 - read in the file to an array with EOL set to \r\n
> > >
> > > Well, in BioPerl the SeqIO system has to deal with files that
> > > easily exceed hundreds of MB :-)
> > >
> > > 	Hilmar
> > 
> > i realize that  - however - 
> > you don't have to read the whole file into an array, just a few lines is 
> > sufficient to determine the EOL.  Hopefully the EOL does not change in the 
> > same file.
> 
> I don't think we can do file "sniffs" like this because often you are
> reading from pipes etc.
> 
> 
> I feel like... well... just saying "it works on UNIX". I guess that's a
> little small-minded right?

The fix (on unix) is to dos2unix the file beforehand.  We can leave this
bug for later if no one wants to play with it.  I'm bogged down with other
things and really want us to try and get the release out by March 1.
(reasonable hilmar? )

> 
> 
> PS - I am about to get into my extension bugs now.
> 
> 
> 
> > 
> > brad
> > 
> > 
> > 
> > _______________________________________________
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/