[Bioperl-l] bpfetch.pl

Aanes Håvard Havard.Aanes at nvh.no
Wed Aug 25 11:47:12 EDT 2010


I am trying do obtain a set of mRNA sequences from a database, made by the bpindex script. I thought this should be a trivial task, but it appears not to be. I get the sequences if I do one by one, like this:

perl scripts/index/bpfetch.pl -dir ./ zebrafish:NM_201192 zebrafish:NM_212708

But I need hundreds of sequences, so my plan was to put the RefSeq IDs in a file and use that as an argument (or whatever it is called in perl). That does not work:

haavaaan at login2 ~/download/src/bioperl-1.2.3 $ perl scripts/index/bpfetch.pl -dir ./ zebrafish:./some_seqs

You are running bpindex.pl without installing bioperl.
You have done it from bioperl/scripts, and so we can find the necessary information
but it is much better to install bioperl

Please read the README in the bioperl distribution

Sequence %id in Database zebrafish is not present

Any suggestions on how to do this? Alternative approaches are also appreciated.

I have no experience in perl, just started using linux, and for the moment there is no time to learn perl, so I would really be grateful for any help to solve this specific task.

Best regards

Håvard Aanes (M.Sc.)
Ph.D. student
Section for biochemistry and physiology
The Norwegian School of Veterinary Science
Telephone: +47 22597358

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