[Bioperl-l] help about Fasta file???

issam outaleb outaleb at web.de
Mon Oct 1 07:46:08 EDT 2007

hallo all,
i have a little problem,:

im using this programm,

i got some experiment and get some results--> IPI hits,(IPI Accnum)

what i want is how can i correlate this IPI ACC Numbers with the FASTA FILE (database fasta),so the programm

has to look where is the IPI Accnum in the db and copy this include description and Sequence to a new file;


#!/usr/bin/perl#use warning;#use strict;use CGI qw(:all);open (IN,"C:/Documents and Settings/XXX/Desktop/Search_file") or die "Fehler beim oeffnen";open (FASTA_db,"C:/Documents and Settings/XXX/Desktop/FASTA1.fasta") or die "FASTA nicht möglich zum öffnen!!" ;open (OUT,">C:/Documents and Settings/XXX/Desktop/reslut.txt") or die "Fehler beim Anlegen der neuen Datei";#print "\nDateien zum kopieren geoeffnet\n";while (<IN>){        $i = $_;        chomp $i;        if(/Hit\d">([^<\/A> ]*)/)#match string from htm datei,give me such result-->IOP123234(just IPIs)     {        #print OUT $1."\n"; #print this IPIs in this file.

 #what i thought was to push up this IPIs in the array than look at them in the fasta_db file and copy it to new file with the description

#and Sequence also. so generate a new fasta file include just my IPIs results.  how???    

		 $j = $1;                push(@array,$j);             }             }       while (defined($var=<suchdatei>)){

$var =~ /(>IPI:)([^| .]*)([^>]*)/   ;#    }} close (IN);close (FASTA_db);close (OUT);print "\nDateien  geschlossen, Kopiervorgang 


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