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Re^2: Find overlap

by linseyr (Acolyte)
on Oct 14, 2012 at 16:46 UTC ( #998963=note: print w/ replies, xml ) Need Help??


in reply to Re: Find overlap
in thread Find overlap

Sorry but im pretty new with perl so I dont really know what this code does. Could you give me some explanation? And why do I get the error: Too many keys when I try to run it? Thanks.


Comment on Re^2: Find overlap
Re^3: Find overlap
by jwkrahn (Monsignor) on Oct 16, 2012 at 04:51 UTC

    The code uses the bit-wise OR operator (|) to turn all bytes in the string in the range to the character '1'.

    And why do I get the error: Too many keys when I try to run it?

    The keys of %data represent the first column of the data files ('chr1') so if you get that error message it means that there was something other than 'chr1' in one of the files.

    After thinking about the problem, and rereading it, it seems that ALL files must overlap so this may work better:

    #!/usr/bin/perl use warnings; use strict; @ARGV = ( '148Nsorted.bed', '162Nsorted.bed', '174Nsorted.bed', '175Ns +orted.bed' ); my ( $bit_mask, %data ) = 1; while ( <> ) { /^\s*(\S+)\s+(\d+)\s+(\d+)\s*$/ or next; $data |= chr( 0 ) x ( $2 - 1 ) . chr( $bit_mask ) x ( $3 - ( $2 - +1 ) ); $bit_mask <<= 1; } keys( %data ) == 1 or die "Error: too many keys: @{[ keys %data ]}\n"; my ( $name, $string ) = each %data; $string =~ /\x0f/ or die "Error: no overlap on all files."; $string =~ /[^\0]/ and my ( $start, $end ) = ( $+[ 0 ], length $string + ); print "$name\t$start\t$end\n";

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