cowboyrocks has asked for the wisdom of the Perl Monks concerning the following question:

Hi Monks,
I need some clue about howto format this sample case. How can I run the if loop in reverse ? I guess that may solve the problem ... :-)
My input looks like this:- 
NT_113797    CDS    122829    123323    -  gene=LOC644591  ProteinID=X
+P_932799.1  
NT_113798    CDS    4457    4636    - 
NT_077932    CDS    9894    9928    - 
NT_077932    CDS    65297    65828    + 
NT_077932    CDS    89196    89690    -  gene=LOC653505  ProteinID=BJD
+ND993

[download]
My output looks like this:- 
NT_113797    CDS    122829    123323    -    
NT_113798    CDS    4457    4636    -  gene=LOC644591
NT_077932    CDS    9894    9928    -  gene=LOC644591
NT_077932    CDS    65297    65828    +  gene=LOC644591
NT_077932    CDS    89196    89690    -  gene=LOC644591

[download]
I want it to be like this:- 
NT_113797    CDS    122829    123323    -  gene=LOC644591 
NT_113798    CDS    4457    4636    -  gene=LOC653505
NT_077932    CDS    9894    9928    -  gene=LOC653505
NT_077932    CDS    65297    65828    +  gene=LOC653505
NT_077932    CDS    89196    89690    -  gene=LOC653505

[download]
My code looks something like this:- 
#!/usr/bin/perl
use warnings;
use strict;

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


{
     my $geneName = "";     

while(<FH>)
 {
       if($_ =~ /\A(\S+)\t(\S+)\t(\d+)\t(\d+)\t(\S)\s+$/)
       {
             print "\n$_ $geneName";
       }
       if($_ =~ /\A(\S+)\t(\S+)\t(\d+)\t(\d+)\t(\S)\s+(\S+)\s+(\S+)\s+
+/)
       {
           $geneName = $6;  
       }
 }
   
}

[download]
Thanks in advance
cowboy :-)

Replies are listed 'Best First'.
Re: Parsing help
by GrandFather (Saint) on Apr 01, 2009 at 04:04 UTC

    Since it's not clear from your sample data where the tabs ought be (and it doesn't matter for demonstration purposes anyway) I've changed the sample code to use spaces instead and changed it to get input from the __DATA__ section:

    use strict;
use warnings;

my @partsList;

push @partsList, [split] while <DATA>;

my $geneName = '';

$geneName = $_->[5] ||= $geneName for reverse @partsList;
print join ("\t", @{$_}[0 .. 5]), "\n" for @partsList;

__DATA__
NT_113797    CDS    122829    123323    -  gene=LOC644591  ProteinID=X
+P_932799.1  
NT_113798    CDS    4457    4636    -
NT_077932    CDS    9894    9928    -
NT_077932    CDS    65297    65828    +
NT_077932    CDS    89196    89690    -  gene=LOC653505  ProteinID=BJD
+ND993

    [download]

    Prints:

    NT_113797    CDS    122829    123323    -    gene=LOC644591
NT_113798    CDS    4457    4636    -    gene=LOC653505
NT_077932    CDS    9894    9928    -    gene=LOC653505
NT_077932    CDS    65297    65828    +    gene=LOC653505
NT_077932    CDS    89196    89690    -    gene=LOC653505

    [download]
    True laziness is hard work
[reply]
[d/l]
[select]

      Very elegant solution, but may has the drawback of having to load the whole file in memory and traverse the whole list 3 times (1 - reading, 2 - filling the field #5 and 3 - printing).

      Since the size of this kind of genomic files may be an issue, here is another version a bit more resource-friendly:

      use strict;
use warnings;

my @acc = ();
while (<DATA>) {
  my @recs = split;
  push @acc, [@recs];
  if (my $geneName = $recs[5]) {
    print join ("\t", @{$_}[0 .. 4], $geneName, "\n") for @acc;
    @acc = ();
  }
}


__DATA__
NT_113797    CDS    122829    123323    -  gene=LOC644591  ProteinID=X
+P_932799.1  
NT_113798    CDS    4457    4636    -
NT_077932    CDS    9894    9928    -
NT_077932    CDS    65297    65828    +
NT_077932    CDS    89196    89690    -  gene=LOC653505  ProteinID=BJD
+ND993

      [download]

      Outputs the desired result:

      NT_113797       CDS     122829  123323  -       gene=LOC644591
NT_113798       CDS     4457    4636    -       gene=LOC653505
NT_077932       CDS     9894    9928    -       gene=LOC653505
NT_077932       CDS     65297   65828   +       gene=LOC653505
NT_077932       CDS     89196   89690   -       gene=LOC653505
p

      [download]

      Hope this helps

      citromatik

[reply]
[d/l]
[select]
Re: Parsing help
by Anonymous Monk on Apr 01, 2009 at 03:39 UTC
    FWIW, that seems like the wrong approach to take. You should be using something that actually knows how to parse that record format (BioPerl ...).

    Now to your code, gene=LOC653505 comes after gene=LOC644591, so you have to parse the file twice, example: 

    #!/usr/bin/perl --

use strict;
use warnings;

sub scan_gene {
    my $fh = shift;
    my $tell = tell $fh;
    my @gene;
    while(readline $fh){
        push @gene, $1 if /gene=(\S+)/;
    }
    seek $fh, $tell, 0;
    return @gene;
}

my @gene = scan_gene(\*DATA);
my $geneix = 0;

#warn "@gene";

while(<DATA>){
    my( $before, $sign, $after ) = split /([+-])/, $_, 2;
    print "$before $sign $gene[$geneix]\n";
    $geneix++ if index($after, $gene[$geneix]) != -1;
#    warn "before $before\nsign $sign\nafter $after";
}


__DATA__
NT_113797    CDS    122829    123323    -  gene=LOC644591  ProteinID=X
+P_932799.1  
NT_113798    CDS    4457    4636    - 
NT_077932    CDS    9894    9928    - 
NT_077932    CDS    65297    65828    + 
NT_077932    CDS    89196    89690    -  gene=LOC653505  ProteinID=BJD
+ND993

    [download]
[reply]
[d/l]

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