On 11-10-12 10:01 AM, Nathalie Conte wrote:
HI All,
I have 2 sets of files I want to compare,and I don't know where to start
to get what I want :(
I have a reference file ( see ref for example) with a chromosome name, a
start and a end position
Chr7 115249090 115859515
Chr8 25255496 29565459
Chr13 198276698 298299815
ChrX 109100951 109130998
and I have a file (file_test) file I want to parse against this
reference ref.txt
Chr1 115249098 Chr1 1362705 Chr8 25255996 Chr8 1362714 Chr1 1362735 ChrX
109100997
So if the position on the file_test is found in ref_file it is kept in a
new file, if not discarded.
I am looking for advises /modules I could use to compare those 2 files .
many thanks in advance for any tips
Nat
Try:
#!/usr/bin/env perl
use strict;
use warnings;
# file names; change as needed
my $ref_file = 'ref.txt';
my $data_file = 'test.txt';
# a hash for hold the start and end positions from the ref file
my %ref = ();
# main
load_ref();
scan();
# load the ref file into %ref
sub load_ref {
open my $ref_fh, '<', $ref_file or die "could not open $ref_file: $!\n";
while( my $line = <$ref_fh> ){
# extract the items from the line
my ( $id, $start, $end ) = split ' ', $line;
# store as HoH
$ref{$id} = {
start => $start,
end => $end,
};
}
close $ref_fh;
}
sub scan {
open my $data_fh, '<', $data_file or die "could not open $data_file:
$!\n";
while( my $line = <$data_fh> ){
# extract each pair of IDs and numbers
while( $line =~ m{ \s* (\S+) \s* (\S+) }gmsx ){
my $id = $1;
my $number = $2;
# see if the number is between the start and end
if( exists $ref{$id}
&& $ref{$id}{start} <= $number
&& $number <= $ref{$id}{end}
){
printf "%-7s % 15s\n", $id, $number;
}
}
}
close $data_fh;
}
__END__
--
Just my 0.00000002 million dollars worth,
Shawn
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Programming is as much about organization and communication
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