[Bioperl-l] about genpept and genbank

Dimitar Kenanov dimitark at bii.a-star.edu.sg
Mon Nov 29 07:17:50 UTC 2010

hi guys,
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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