[Bioperl-l] extract ORF ID from fasta file using bioperl

Jason Stajich jason.stajich at gmail.com
Fri Oct 21 05:56:11 EDT 2011


easy to do this with a simple regular expression and opening a new file.  Have you read up on this concept in Perl. 
You can use SeqIO to parse FASTA files - did you read the HOWTO and website documentation first?

We don't typically do people's work for them on this mailing list so please show some effort first.

On Oct 20, 2011, at 10:59 PM, Shachi Gahoi wrote:

> Dear all,
> 
> I have fasta format sequence file and I want to extract ORF ID "PITG_14194"
> from fasta file and then I want to rename same file with that ORF ID
> "PITG_14194".
> 
> I have many files and I want to do same exercise with all sequence files.
> 
> Please tell me how can i do this with perl or bioperl.
> 
>> tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora
> infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1
> MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL
> ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA
> RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF
> HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM
> YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL
> TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD
> RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR
> NGIAVDHKGVICNGKAPIEIAVDENTLSAAA
> 
> 
> -- 
> Regards,
> Shachi
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