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";
}
}
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Gunnar Hjalmarsson
Email: http://www.gunnar.cc/cgi-bin/contact.pl
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