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

[Carnë Draug]

On 3 November 2011 12:12, pankaj <pankajt322 at gmail.com> wrote:
>
>
> On Oct 21, 1:59 am, Shachi Gahoi <shachigahoi... at gmail.com> 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
>>

---------- Forwarded message ----------
From: Jason Stajich <jason.stajich at gmail.com>
Date: 21 October 2011 10:56
Subject: Re: [Bioperl-l] extract ORF ID from fasta file using bioperl
To: Shachi Gahoi <shachigahoimbi at gmail.com>
Cc: bioperl-l at bioperl.org


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.