Hi Monks,
I am trying to parse a large file and filter according the fields I require.
My code looks like this:-

#!/usr/bin/perl

$fn = $ARGV[0];
open(FH, "$fn") || die("cannot open:$!");

          $\ = ' '; 
while(<FH>)
 {     
   
           $\ = "\n" if eof;
           chomp($_);
           $_ =~ s/\(|\)//xmg;
           if($_ =~ /LOCUS\s+(\S+)/) { $gi=$1; }
           elsif($_ =~ /\A\s+(\w+)\s+(\S+)\.\.(\S+)/) { print "\t\t$gi
+\t$1\t$2\t$3\n"; }
           elsif($_ =~ /gene\=\"(\S+)\"/) { print "\t\t$gi\t\t\t\t\tge
+ne=$1\n"; }
           elsif($_ =~ /\/transcript_id\=\"(\S+)\"/) {print "\t\t$gi\t
+\t\t\t\tTranscriptID=$1\n";}

 }
[download]

Input looks like below:-

     gene         348634..348822
                     /gene="LOC100129305"
                     /note="Derived by automated computational analysi
+s using
                     gene prediction method: GNOMON. Supporting eviden
+ce
                     includes similarity to: 1 Protein"
                     /db_xref="GeneID:100129305"
     mRNA         348634..348822
                     /gene="LOC100129305"
                     /product="similar to C21orf94 protein"
                     /note="Derived by automated computational analysi
+s using
                     gene prediction method: GNOMON. Supporting eviden
+ce
                     includes similarity to: 1 Protein"
                     /transcript_id="XM_001714760.1"
                     /db_xref="GI:169215265"
                     /db_xref="GeneID:100129305"
[download]

My ouput is coming like this(tab separated):-

           gene   348634   348822   
                                 gene=LOC100129305
           gene   348634   348822
                                 gene=LOC100129305
                                 TranscriptID=XM_001714760.1
[download]

Whereas I want it to come like like:-

           gene   348634   348822   gene=LOC100129305
           gene   348634   348822   gene=LOC100129305    TranscriptID=
+XM_001714760.1
[download]

Thanks in advance
cowboy :)

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