perlquestion
jemswira
<p>Hi there monks. </p>
<p>I'm trying to combine two databases into one for my computational bio project. The first database (Test) looks something like this:</p>
<code> Q197F8 ORFNames=IIV3-002R
Q197F7 ORFNames=IIV3-003L
Q6GZX2 ORFNames=FV3-003R
Q6GZX1 ORFNames=FV3-004R
Q197F5 ORFNames=IIV3-005L
Q6GZX0 ORFNames=FV3-005R ;PF02393
Q91G88 ORFNames=IIV6-006L ;PF12299;PF04383
Q6GZW9 ORFNames=FV3-006R
</code>
<p>It's just a small part of it.
The .{6} before the ORFNAMES is the accession numbers. Next I have this sort of format in Test2.</p>
<code>Q197F8 | PF04947.9
Q91G88 | PF01486.12 PF00319.13</code>
<p>The format I need in the end is this:</p>
<code>Q197F8 IIV3-002R PF04947.9
Q91G88 IIV6-006L PF01486.12 PF00319.13</code>
<p> Since the first database test was going to be much larger than the second, I wanted to make it into an array list with the accession numbers and names, then go down the list of accession numbers in Test2 and print them out. Like so: </p>
<code>
#!/usr/bin/perl
use warnings;
use strict;
open DATA, "C:\\Users\\Jems\\Desktop\\Perl\\test\\test.txt" or die $!;
use Modern::Perl;
use Data::Dump qw/dump/;
our %data;
my $ac;
while (<DATA>) {
my @splitted= split(/=|;/);
foreach (@splitted){
if (/^(.{6})\sORFNames/) {
$ac = $1;
chomp ($ac);
next;
}
if (/^(.+)\s\n/) {
#print "$ac $1\n";
push @{ $data{$1} }, $ac;
next;
#print @{$data{$ac}} if exists $data{$ac};
}
if (/^(.+)\s;PF/) {
push @{ $data{$1} }, $ac;
next;
}
next;}
next;
}
my $acn;
open ACTIVATOR, "C:\\Users\\Jems\\Desktop\\Perl\\test\\Test2.txt" or die $!;
open ACTIVOUT, ">C:\\Users\\jems\\Desktop\\Perl\\test\\ActivACNPF.txt" or die $!;
select ACTIVOUT;
while ($acn= <ACTIVATOR>){
if($acn =~ m/^(......)\s\|/){
my $ab = $1;
chomp ($ab);
#print "$ab";
print "$acn | @{$data{$ab}}\n" if exists $data{$ab};
next;
}
}
print STDOUT "DONE ACTIV";
</code>
<p> The commented parts were my print testing. However I just can't seem to get the print at line 44 to print what I want. the commented print at line 23 returns blank, but the commented print at line 19 prints that both are correct. Also, if I use a print %data, it will return values. Am I checking something wrongly? </p>
<p> Thanks monks!</p>