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.
Håvard Aanes (M.Sc.)
Section for biochemistry and physiology
The Norwegian School of Veterinary Science
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