[Bioperl-l] HOW TO PRINT SOME INFORMATION FROM A BLAST_OUTPUT.TXT FILE TO A NEW FASTA.TXT FILE

Frank Schwach fs5 at sanger.ac.uk
Wed Jan 11 09:50:01 EST 2012


Hi Paulos,

have a look at the tutorial for using Bio::SearchIO:

http://www.bioperl.org/wiki/HOWTO:SearchIO#Creating_Reports_for_SearchIO

Under "Using SearchIO" you will see the generic script for getting 
information out of BLAST reports. You will see how to get each alignment 
shown in the report and access the information associated with it.
Printing FASTA is very easy as you only need something like

print ">$id\n$sequence\n";

but you can also look at the HOWTO for Bio::SeqIO 
(http://www.bioperl.org/wiki/HOWTO:SeqIO) to do it the BioPerl way.

Frank



On 11/01/12 13:04, paulos wrote:
> GREETINGS TO ALL,
> THIS IS THE BLAST_OUTPUT .TXT FILE :
> http://old.nabble.com/file/p33120359/blast_output.txt blast_output.txt
> I WANT TO PRINT TO A NEW FILE NAMED AS FASTA.TXT THE PROTEINS' SEQUENCES
> MATCHED IN THE BLAST_OUTPUT FILE WITH SIMPLE PERL SCRIPT.
>
> THANKS IN ANDVANCED.


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


More information about the Bioperl-l mailing list