May be this'll help? )
#!/usr/bin/perl
use strict;
use warnings;
die 'Usage: ' . __FILE__ . " file1[ file2...]\n" unless @ARGV;
my $ref_file = 'ref.txt';
my $new_file = 'new.txt';
open my $ref_fh, '<', $ref_file
or die "Failed to open reference file - $!\n";
my %limits_for;
while (<$ref_fh>) {
next unless /\d/; # skipping infoless lines
my ($chromosome, $start, $end) = split;
$limits_for{ $chromosome } = {
start => $start,
end => $end,
};
}
close $ref_fh;
my %positions_for;
while (<>) {
my ($chromosome, $pos) = split;
push @{ $positions_for{ $chromosome } }, $pos;
}
my %in_limits_for;
foreach my $chromosome (keys %positions_for) {
next unless exists $limits_for{ $chromosome };
my @in_limits = grep {
$limits_for{ $chromosome }->{start} <= $_
&&
$_ <= $limits_for{ $chromosome }->{end}
} @{ $positions_for{ $chromosome } };
$in_limits_for{ $chromosome } = \@in_limits;
}
open my $new_fh, '>', $new_file
or die "Failed to write out results - $!\n";
foreach my $chromosome (keys %in_limits_for) {
foreach my $pos ( @{ $in_limits_for{ $chromosome } } ) {
printf $new_fh
"%-7s %15s\n", $chromosome, $pos;
}
print $new_fh '=' x 80 . "\n";
}
close $new_fh;
-- iD
2011/10/12 Nathalie Conte <n...@sanger.ac.uk>
> 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
>
>
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