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

Shachi Gahoi shachigahoimbi at gmail.com
Fri Oct 21 01:59:12 EDT 2011


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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