Re^3: hash with both values and keys unique to each other

Following is the real code :

use strict;
use Time::HiRes;
my $start_time = [Time::HiRes::gettimeofday()];
my (@coordinates,%hash_chr,%HOA,%HOH,%hash_line) = ();
open FILE,"GmGm.recent.gff";
while(my $line=<FILE>){
chomp $line;
my %seen = ();

if($line=~/^(Gm\d{1,})\trecent_duplication\tsyntenic_region\t(\d{1,})\
+t(\d{1,})\t.*\tID\=\w{1,}_Gm\d{1,}\.(Gm\d{1,}.*)\;median_Ks=(.*)\;mat
+ches\=(Gm\d{1,}\:\d{1,}\.\.\d{1,})/)
{
    my $chr1 = "$1:$2..$3";
    my $ks_val = $5;
    my $chr2 = $6;
    
    if ((exists $hash_chr{$chr2})&&($ks_val > 0.4)){
       next;
    }    
    else{
          $hash_chr{$chr1}=$chr2;
      }
      }
}
close FILE;
[download]

And this is how the file looks like


Gm01    recent_duplication    syntenic_region    170877    269340    1
+79    -    .    ID=A_Gm01.Gm08.2.-;median_Ks=0.1101;matches=Gm08:4628
+8465..46349001

Gm08    recent_duplication    syntenic_region    46288465    46349001 
+   179    -    .    ID=B_Gm01.Gm08.2.-;median_Ks=0.1101;matches=Gm01:
+170877..269340
[download]

Comment on Re^3: hash with both values and keys unique to each other Select or Download Code

Replies are listed 'Best First'.
Re^4: hash with both values and keys unique to each other by hbm (Hermit) on Jul 12, 2012 at 19:38 UTC
As a side note, you can clean up that regex quite a bit by using `+` instead of `{1,}`, and not escaping colons, semi-colons, and equals: `#if($line=~/^(Gm\d{1,})\trecent_duplication\tsyntenic_region\t(\d{1 +,})\t(\d{1,})\t.\tID\=\w{1,}_Gm\d{1,}\.(Gm\d{1,}.)\;median_Ks=(.)\ +;matches\=(Gm\d{1,}\:\d{1,}\.\.\d{1,})/) if($line=~/^(Gm\d+)\trecent_duplication\tsyntenic_region\t(\d+)\t(\ +d+)\t.\tID=\w+_Gm\d+\.(Gm\d+.);median_Ks=(.);matches=(Gm\d+:\d+\.\ +.\d+)/)` [download]	[reply] [d/l] [select]
Re^5: hash with both values and keys unique to each other by Anonymous Monk on Jul 12, 2012 at 22:18 UTC
You could clean it up quite a bit more by splitting the line on tabs and parsing each of the columns individually...	[reply]