Dear all, This is related to an earlier post, and I have made progress, but I am stuck again. I am parsing a file (partial example below), and reading into a hash %values. However, I want to extract info from the Ecogene line (eg. DBLINKS - (ECOGENE)). I think my %values hash will not have separate vale/record pairs for the 5 different DBLINKS. Is there anyway I can just extract the one for ECOGENE. I tried one way in my code, but it is wrong as I realize the problem is in reading into the hash. Any help appreciated.

portion of input file

//
UNIQUE-ID - EG11751
TYPES - BC-5.5.2
TYPES - BC-1.7.9
TYPES - BC-5.5.1
COMMON-NAME - otsA
ACCESSION-1 - b1896
ACCESSION-2 - ECK1895
CENTISOME-POSITION - 42.636864    
COMMENT-INTERNAL - 1/24/05 keseler removed pexA as synonym
COMPONENT-OF - COLI-K12-39
COMPONENT-OF - TU0-7722
COMPONENT-OF - TU00391
COMPONENT-OF - TU00312
DBLINKS - (ECOLIHUB "otsA" NIL |kr| 3474243543 NIL NIL)
DBLINKS - (REGULONDB "EG11751" NIL |kr| 3462030648 NIL NIL)
DBLINKS - (ASAP "ABE-0006318" NIL |paley| 3398447608 NIL NIL)
DBLINKS - (ECHOBASE "EB1701" NIL |pkarp| 3346767936 NIL NIL)
DBLINKS - (ECOGENE "EG11751" NIL |pick| 3292798423 NIL NIL)
DBLINKS - (OU-MICROARRAY "b1896" NIL NIL NIL NIL NIL)
DBLINKS - (CGSC "18073" NIL |pkarp| 3035559680 NIL NIL)
KNOCKOUT-GROWTH-OBSERVATIONS - OBS0-40
KNOCKOUT-GROWTH-OBSERVATIONS - OBS0-37
KNOCKOUT-GROWTH-OBSERVATIONS - OBS0-33
KNOCKOUT-GROWTH-OBSERVATIONS - OBS0-49
KNOCKOUT-GROWTH-OBSERVATIONS - OBS0-44
LAST-UPDATE - 3609256889
LEFT-END-POSITION - 1978212
MEMBER-SORT-FN - NUMBERED-CLASS-SORT-FN
PRODUCT - TREHALOSE6PSYN-MONOMER
RIGHT-END-POSITION - 1979636
TRANSCRIPTION-DIRECTION - -
//

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code

use strict;
use warnings;
use Data::Dumper;
##
my $inGeneDat=$ARGV[0] || "genes.dat";
open(IN,"<",$inGeneDat) || die "cannot open $inGeneDat\n";

##
my %HoNms;
{
  local $/ = '//';
  while(my $record=<IN>)
  {
    my %values = $record =~ /^(\S+)\s+-\s+(\S+)/mg;
    next unless exists $values{'UNIQUE-ID'} and exists $values{'ACCESS
+ION-1'};
    # Your code using $values{'UNIQUE-ID'} and other values here
        my $cycID=$values{'UNIQUE-ID'};
        my $cycLoc=$values{'ACCESSION-1'};
        my $ECKLoc=$values{'ACCESSION-2'};
        my $EGLocL=$values{'DBLINKS'};
        $EGLocL=~/"(EG\S+)"/;
        my $EGLoc=$1;
        my $Nm=$values{'COMMON-NAME'};
        #
        $HoNms{$cycID} = { 'acc1' => $cycLoc,
                 'acc2' => $ECKLoc,
                'EG'=> $EGLoc,
                'nm' => $Nm
               };
  }
}

print Dumper(%HoNms);
close(IN);

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In reply to file parsing by AWallBuilder

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