Dear All,

I am trying to parse a file in a while loop and printing some matched regular expression parameters.

Below is my code and data file 

my $filename =  test.summary";
open (IN, "<", $filename) or die "Check the summary file. $!\n";
while (my $line = <IN>) {
    chomp $line;
    if ($line =~/^LOCUS\s+\w+\d+\s+(\d+)\sbp/) {
        $gene_length = $1;
    }
    if ($line =~/^DEFINITION\s+(.*)/s) {
        $definition = $1;
    }
    if ($line =~/^ACCESSION\s+(.*?)\s+/) {
        $accession = $1;
    }
    if ($line =~ /\s+\/db_xref="GI\:(\d+)\"/) {
        $gi_number = $1; 
    }
    if ($line =~ /\s+\/db_xref=\"GeneID\:(\d+)\"/) {
        $gene_id = $1;
    }
}

[download]
 
Data file:
LOCUS       NM_001098209            3415 bp    mRNA    linear   PRI 27
+-APR-2014
DEFINITION  Homo sapiens catenin (cadherin-associated protein), beta 1
+, 88kDa
            (CTNNB1), transcript variant 2, mRNA.
ACCESSION   NM_001098209 XM_001133660 XM_001133664 XM_001133673 XM_001
+133675
VERSION     NM_001098209.1  GI:148233337
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Eutele
+ostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhin
+i;
            Catarrhini; Hominidae; Homo.
     CDS             269..2614
                     /gene="CTNNB1"
                     /gene_synonym="armadillo; CTNNB; MRD19"
                     /codon_start=1
                     /product="catenin beta-1"
                     /protein_id="NP_001091679.1"
                     /db_xref="GI:148233338"
                     /db_xref="CCDS:CCDS2694.1"
                     /db_xref="GeneID:1499"
                     /db_xref="HGNC:HGNC:2514"
                     /db_xref="MIM:116806"
                     /translation="MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGI
+HSGATTTAP
                     SLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQR
+VRAAMFPET
                     LDEGMQIPSTQFDAAHPTNVQRLAEPSQMLKHAVVNLINYQDDAELATR
+AIPELTKLL
//

[download]

My questions:

a) How can I parse the multiline DEFINITION in the while loop as the regular expression captures only the first line .

b) Could I get some help in capuring the content of CDS block and then parse individual entries one by one( like GI, GeneID etc.).

I am trying to learn using Perl only so I am not using the BioPerl module for the above purpose.

Regards

In reply to multiline in while loop and regular expression by newtoperlprog

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