[Bioperl-l] about genpept and genbank
dimitark at bii.a-star.edu.sg
Mon Nov 29 07:17:50 UTC 2010
i dug up a bit more and found a solution. i think the problem is that in
'download_query_genbank.pl' there is the 'format' option which only is
responsible for the format of the output file to which seqs are
downloaded. While i need 'ret_type' format option according to NCBI
Eutils. So now i found that i can use GenBank.pm for all DBs in NCBI. I
restored the GenPept as it was in original but i do not use it, its more
tricky than GenBank.pm. Now modified 'download_query_genbank.pl' to use
only GenBank and added one more option 'retformat' which can be set
according to NCBI 'rettype'. Also added a simple progress bar to follow
the download. Unfortunately it is working only if im downloading genbank
data(Bio::SeqIO::genbank) when i download fasta(Bio::SeqIO::fasta) i
cant use it. Seems that the fasta stream is a big chunk or somewhere the
flush is set to zero. I dont know yet, still trying to figgure that out.
The modified script is attached.
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