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Re: How to process a BED file as chunk of lines based on chromosome names

by GrandFather (Saint)
on Jul 20, 2021 at 01:34 UTC ( #11135184=note: print w/replies, xml ) Need Help??


in reply to How to process a BED file as chunk of lines based on chromosome names

Rather than using manifest variables for accumulating results you can use a hash keyed by chromosome:

use strict; use warnings; my %chroms; # Count frequency of start sited in the column-2. while (<DATA>) { next if /^#/; #ignore comments in the input file chomp(my $line = $_); my ($chr, $start, $end, $strand) = (split /\t/, $line)[0, 1, 2, 5] +; my $startPoint; if ($strand eq '+') { $startPoint = $start; $chroms{$chr}{startPoints_plusStrand}{$startPoint}++; } elsif ($strand eq '-') { $startPoint = $end; $chroms{$chr}{startPoints_minusStrand}{$startPoint}++; } else { die "Goofy BED Data on line $.:\n$_"; } } print "#Plus Strand BedGraph:\n"; for my $chromKey (keys %chroms) { my $chrom = $chroms{$chromKey}; print "--- $chromKey\n"; for my $key (sort {$a <=> $b} keys %{$chrom->{startPoints_plusStra +nd}}) { print $key + 1, "\t", "+", "$chrom->{startPoints_plusStrand}{$ +key}\n"; } } __DATA__ #chromosome start end position col-5 strand chr7 127471196 127472363 Pos1 0 + chr7 127471196 127472363 Pos1 0 + chr7 127471196 127472363 Pos1 0 + chr7 127471196 127472363 Pos1 0 + chr7 127471196 127472363 Pos1 0 + chr7 127472363 127473530 Pos2 0 + chr7 127473530 127474697 Pos3 0 - chr7 127474697 127475864 Pos4 0 - chr8 40000 40500 Pos5 0 + chr8 40000 40600 Pos5 0 + chr8 40000 40650 Pos5 0 + chr8 41000 41200 Pos6 0 -
Optimising for fewest key strokes only makes sense transmitting to Pluto or beyond
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