[Bioperl-l] extract ORF ID from fasta file using bioperl
Shachi Gahoi
shachigahoimbi at gmail.com
Fri Oct 21 05:59:12 UTC 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
More information about the Bioperl-l
mailing list