Got it.Thanks.I have been able to retrive all the info i need and in
the format that I want.
Now I need some light on the following.
Here is a snippet again:
gene 410..1750
> > /gene="dnaA"
> > /db_xref="EMBL:2632267"
> > CDS 410..1825
> > /gene="dnaA"
> > /function="initiation of chromosome replication (DNA
> > synthesis)"
> > /note="alternate gene name: dnaH, dnaJ, dnaK"
> > /codon_start=1
> > /transl_table=11
> > /protein_id="CAB11777.1"
> > /db_xref="GI:2632268"
I have range1..range1
range2..range2
The start of all the 2 range is same.The ending number is differnent.I
need to compute the difference in the two and display it with the gene
name: example for this snippet:
dnaA:75
I need an idea as to how to tie the gene name with the diff. value.
Thanks a lot,
On 12/4/07, Gunnar Hjalmarsson <[EMAIL PROTECTED]> wrote:
> minky arora wrote:
> > .A part of my file looks like this:
> >
> > gene 410..1750
> > /gene="dnaA"
> > /db_xref="EMBL:2632267"
> > CDS 410..1750
> > /gene="dnaA"
> > /function="initiation of chromosome replication (DNA
> > synthesis)"
> > /note="alternate gene name: dnaH, dnaJ, dnaK"
> > /codon_start=1
> > /transl_table=11
> > /protein_id="CAB11777.1"
> > /db_xref="GI:2632268"
> >
> > I need to extract the range for gene as well as CDS and compare them.
> >
> > SO far this is where Ive reached:
> > #!/usr/bin/perl
> > use warnings;
> > use strict;
> > my $line;
> > my @new;
> > my $line1;
> > open FILE,"/users/meenaksharora/bio.txt"or die"cannot open $!\n";
> > foreach $line(<FILE>){
> > if($line=~m/gene/)
> > [EMAIL PROTECTED];
> > }
> > }
>
> At this point, @new contains one element with the _last_ line containing
> the substring 'gene'.
>
> Maybe you want to anchor the regex:
>
> if ( $line =~ m/^gene/ )
> --------------------^
>
> > foreach $line1(@new){
> > if($line1=~m/(\d)+\.\./)
> > { print $line1;print "hello";
> > }
> > }
>
> You may also want to replace those foreach loops with:
>
> while ( $line = <FILE> ) {
> if ( $line =~ /(gene|CDS)\s+(\d+\.\.\d+)/ ) {
> print "$1: $2\n";
> }
> }
>
> --
> Gunnar Hjalmarsson
> Email: http://www.gunnar.cc/cgi-bin/contact.pl
>
> --
> To unsubscribe, e-mail: [EMAIL PROTECTED]
> For additional commands, e-mail: [EMAIL PROTECTED]
> http://learn.perl.org/
>
>
>
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