[Jalview-discuss] Fwd: Non - Delimited FASTA output

[Jim Procter]

On 26/01/2011 18:23, Ackers, Jared (DEWN) wrote:
>
> Jim,
>
> Thanks for the advice.  I don't think that BioPython has a problem, 
> I've found it very useful to go back and forth between tab delimited 
> and fasta formats when necessary.  I should stress that I only use it 
> as a parser, all other functions are performed elsewhere.  The only 
> minor inconvenience I've found is that it sometimes has problems with 
> long pathlengths.
>
understood - Peter's comment helped clear up the situation.
>
> Sadly, I don't code.  I maintain a rather large flatfile database of 
> annotated sequences, and it is necessary to have the sequence in a 
> single field.  My problem is that occasionally I want to re-upload 
> manipulated sequences to that database.  When I do this, I have to do 
> it with multiple (still quite large) subsets of data, so I'm always 
> looking to loose a step.  If the fasta file contains line feeds, each 
> line of a sequence becomes a new record; and I can't get that program 
> to ignore line feeds.
>
> I've just found that if you open the alignment in MEGA 5 and export as 
> a FASTA (*.mas) file you can eliminate the line feeds.
>
Glad to hear the problem's solved!
Jim.
ps. sounds like you actually wanted the pfam output, which is 
SequenceID<tab><sequence>.


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