Dear all,
I am familiar with how to read in a table, parse the columns and create hashes holding the data . However, now I am dealing with input files where related variables are contained in subsequent rows as opposed to in the same column. Now, I am having a seemingly simple problem that my parsing logic doesn't seem to work anymore. It might be an error to do with when I initialize my variables, or what? Any help is appreciated.
sample input data
#
UNIQUE-ID - GJDZ-5046
TYPES - BC-4
TYPES - Unclassified-Genes
COMMON-NAME - STM14_5042
ACCESSION-1 - STM14_5042
CENTISOME-POSITION - 90.96536
COMPONENT-OF - CHROMOSOME-1-100
COMPONENT-OF - TUJDZ-2494
COMPONENT-OF - CHROMOSOME-1
LEFT-END-POSITION - 4430254
PRODUCT - GJDZ-5046-MONOMER
RIGHT-END-POSITION - 4430427
TRANSCRIPTION-DIRECTION - -
//
UNIQUE-ID - GJDZ-1101
TYPES - BC-4
TYPES - Unclassified-Genes
COMMON-NAME - focA
ACCESSION-1 - STM14_1100
CENTISOME-POSITION - 20.85712
COMPONENT-OF - CHROMOSOME-1-23
COMPONENT-OF - TUJDZ-587
COMPONENT-OF - CHROMOSOME-1
LEFT-END-POSITION - 1015797
PRODUCT - GJDZ-1101-MONOMER
RIGHT-END-POSITION - 1016774
TRANSCRIPTION-DIRECTION - -
//
snippet of code that gives wrong results
my %Ho14Loc2GeNm;
while(my $lines=<IN>){
my $cycID14; my $cycLoc14;my $cycNm14;
next unless (($lines =~/^UNIQUE-ID/) || ($lines=~/^ACCESSION-1
+/)|| ($lines=~/^COMMON-NAME/));
chomp $lines;
if ($lines =~ /^UNIQUE-ID/){
$lines=~/(GJDZ-[0-9]+)/;
$cycID14=$1;
}
if ($lines =~ /^COMMON-NAME/){
$lines=~/COMMON-NAME - (\S+)/;
$cycNm14=$1;
}
if ($lines =~ /^ACCESSION-1/){
$lines=~/(STM14_[0-9]+)/;
$cycLoc14=$1;
}
if (defined($cycLoc14)){
$Ho14Loc2GeNm{$cycLoc14}=$cycNm14;
}
}
print Dumper(%Ho14Loc2GeNm);
close(IN);