How can I read and parse chunks of data into a Perl hash of arrays?
- by neversaint
I have data that looks like this:
#info
#info2
1:SRX004541
Submitter: UT-MGS, UT-MGS
Study: Glossina morsitans transcript sequencing project(SRP000741)
Sample: Glossina morsitans(SRS002835)
Instrument: Illumina Genome Analyzer
Total: 1 run, 8.3M spots, 299.9M bases
Run #1: SRR016086, 8330172 spots, 299886192 bases
2:SRX004540
Submitter: UT-MGS
Study: Anopheles stephensi transcript sequencing project(SRP000747)
Sample: Anopheles stephensi(SRS002864)
Instrument: Solexa 1G Genome Analyzer
Total: 1 run, 8.4M spots, 401M bases
Run #1: SRR017875, 8354743 spots, 401027664 bases
3:SRX002521
Submitter: UT-MGS
Study: Massive transcriptional start site mapping of human cells under hypoxic conditions.(SRP000403)
Sample: Human DLD-1 tissue culture cell line(SRS001843)
Instrument: Solexa 1G Genome Analyzer
Total: 6 runs, 27.1M spots, 977M bases
Run #1: SRR013356, 4801519 spots, 172854684 bases
Run #2: SRR013357, 3603355 spots, 129720780 bases
Run #3: SRR013358, 3459692 spots, 124548912 bases
Run #4: SRR013360, 5219342 spots, 187896312 bases
Run #5: SRR013361, 5140152 spots, 185045472 bases
Run #6: SRR013370, 4916054 spots, 176977944 bases
What I want to do is to create a hash of array with first line of each chunk as keys
and SR## part of lines with "^Run" as its array member:
$VAR = {
'SRX004541' => ['SRR016086'],
# etc
}
But why my construct doesn't work. And it must be a better way to do it.
use Data::Dumper;
my %bighash;
my $head = "";
my @temp = ();
while ( <> ) {
chomp;
next if (/^\#/);
if ( /^\d{1,2}:(\w+)/ ) {
print "$1\n";
$head = $1;
}
elsif (/^Run \#\d+: (\w+),.*/){
print "\t$1\n";
push @temp, $1;
}
elsif (/^$/) {
push @{$bighash{$head}}, [@temp];
@temp =();
}
}
print Dumper \%bighash ;
