[Jalview-discuss] Fwd: Non - Delimited FASTA output
jprocter at compbio.dundee.ac.uk
Wed Jan 26 20:31:57 GMT 2011
On 26/01/2011 18:23, Ackers, Jared (DEWN) wrote:
> 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!
ps. sounds like you actually wanted the pfam output, which is
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