[Biopython-dev] Re: [BioPython] Whitespace in sequences

[Iddo Friedberg]

Hi,

I replaced \n with os.linesep in Bio.FASTA and commited to the CVS.

I can't find the contingency tests for the Bio.SeqIO modules, so I don't 
want to commit those changes before i test them. If anybody can point my 
at the right test_*.py script please?

Iddo


Iddo Friedberg wrote:
> 
> 
> Paul-Michael Agapow wrote:
> 
>>
>> Thanks Iddo,
>>
>>> I guess you were using biopython on a Mac/Windows box, where '\r' or
>>> '\r\n' is a
>>> newline. Also, it looks like you were using the Bio.Fasta package to
>>> read... the bug shouldn't occur within Bio.SeqIO.FASTA.FastaReader
>>> (although it will within SeqIO.FASTA.FastaWriter!)
>>
>>
>>
>> Picked it straight off - I'm using MacOS X. However, I'm using 
>> Bio.SeqIO.FASTA.FastaReader.
> 
> 
> Well that's funny... Jeff, Yair, any comment on this? I believe you have 
> Macs too.
> 
> Which IMHO does not preclude the `\n' --> os.linesep overhaul required. 
> I wonder why this bug was hit upon only now. Thanks very much for 
> reporting this.
> 
> Cheers all,
> 
> Iddo
> 
> 
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
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Tel: +1 (858) 646 3100 x3516
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http://bioinformatics.ljcrf.edu/~iddo