[Bioperl-l] new modules for sarching for patterns in fasta-fi les

Heikki Lehvaslaiho heikki at ebi.ac.uk
Mon Aug 15 09:22:49 EDT 2005

On Tuesday 09 August 2005 20:20, Amir Karger wrote:
> I wrote a simple one-liner to convert fasta to three, tab-separated
> columns: ID (without '>') desc, and concatenated sequence. That way you
> don't have to worry about keeping the two files tied together, but agrep
> should still find things only in the concatenated sequence. (Unless
> somebody mean put a sequence into the description column.) As an added
> bonus, it means you can throw a FASTA into Excel for sorting, filtering,
> etc. Or merge with a gene list pretty easily.
> It's at
> http://cgr.harvard.edu/cbg/scriptome/Tools/Change.html#new__change_a_fasta_
>f ile_into_tabular_format__change_fasta_to_tab_
> along with the tab-to-FASTA converter, along with a couple sentences
> describing potential gotchas (e.g., any tabs in the desc get lost)


FYI, this is  already implemented as 'tab' format in Bio::SeqIO.


More information about the Bioperl-l mailing list