Thanks PAul,
That solves half my problem.I am working on it.If I need more help,I
will post it up.
-Min
On 12/4/07, Paul Lalli <[EMAIL PROTECTED]> wrote:
> On Dec 4, 11:06 am, [EMAIL PROTECTED] (Minky Arora) wrote:
> > I am quite new to perl so pls bear with me.I am trying to do some
> > Bioinformatics Analysis.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];
>
> This line most likely does not do what you think it does. Are you
> trying to add every line that matches 'gene' to the array? That's
> not what this does. This overwrites the existing @new contents,
> setting @new to be the last value of $line that matches 'gene'. In
> your example data, this is the second '/gene="dnaA"' line.
>
> > }}
> >
> > foreach $line1(@new){
>
> So by the time you get to here, @new only has one element in it, and
> you're iterating over that one element - '/gene="dnaA"'. This line
> obviously doesn't have any numbers in it, so the regexp fails.
>
> > if($line1=~m/(\d)+\.\./)
> > { print $line1;print "hello";
> > }
> >
> > }
> >
> > I am not able to extract the lines with the digits.I am not sure
> > why.IS there a better way to do this?? Can someone guide me how to go
> > abt that?
>
> You need better debugging skills, which will likely develop over
> time. You're assuming there's a problem with your regexp, when
> there's actually a problem with your array. If you'd printed the
> contents of your array before the loop, you would have seen that.
>
> change
> @new = $line;
> to
> push @new, $line;
> so that each matching value of $line gets added to the end of @new,
> rather than overwriting the existing contents.
>
> push @new, $line
> means roughly the same thing as
> @new = (@new, $line);
> except it's more efficient.
>
> Think of 'push' as the same sort of shortcut as the .= operator, so
> you can write
> $text .= $string;
> rather than
> $text = $text . $string;
>
> perldoc -f push
> for more information.
>
> Paul Lalli
>
>
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> http://learn.perl.org/
>
>
>
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