Hi Rochak,
the short answer to your question is 'NO'.
As i understand that you have an attribute which contains the sequence.
Somewhere in your output formatter (e,g TSV, CSV etc) you need to hook
this up and rearrange the order of attributes and reformat to comply
with FASTA. I would suggest that you create a formatter of your own
under biomart-perl/lib/BioMart/Formatters/ say FASTA
the best would be to reverse engineer from TSV. All you need is to scan
for the sequence attribute name and convert the whole set of attributes
to FASTA. If you look into the code, its fairly simple.
Hope this is helpful, please do write back in case you need more help.
Cheers
Syed
Rochak Neupane wrote:
fasta output:
Is there a way to generate a fasta output from fields that are not in
GenomicSequence?
We have a longtext field that we would like to be fasta formatted. But
it seems right now only the importables in GenomicSequence get that
format, or perhaps I am missing something?
thanks,
rochak
