On Thu, May 12, 2011 at 10:23:29AM +0100, Nathalie Conte wrote:
<snip>
> I have this file format
> chr start end strand
> x 12 24 1
<snip>
> I have this script to split and iterate over each line, but I don't
> know how to group 2 lines together, and take the start of the firt line
> and the end on the second line? could you please advise? thanks
my $file = 'chrome.dat';
my %hash;
open my $FH, '<', $file or die "Unable to open $file: $!, stopped ";
while( my $line = <$FH> )
{ my ( $chr, $start, $end, $strand ) = split /\s+/, $line;
# on the assumption there might be a chrom. x, strand 2
my $key = $chr . ':' . $strand;
if( exists $hash{$key} )
{ $hash{$key}{'start'} = $start
if( $start < $hash{$key}{'start'} );
$hash{$key}{'end'} = $end
if( $hash{$key}{'end'} < $end );
}
else
{ $hash{$key}{'start'} = $start;
$hash{$key}{'end'} = $end;
}
}
close $FH or die "Unable to close $file: $!, stopped ";
my $outfile = 'chrome_out.dat';
open my $OFH, '>', $outfile or die "Unable to open $outfile: $!, stopped ";
for my $k (sort keys %hash)
{ my ( $chr, $strand) = split /:/, $k;
printf $OFH "%s\t%s\t%s\t%s\n",
$chr, $hash{$k}{'start'}, $hash{$k}{'end'}, $strand;
}
close $OFH or die "Unable to close $outfile: $!, stopped ";
HTH,
Mike
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