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gpertea |
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#!/usr/bin/perl |
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use strict; |
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my $usage=q/Usage: |
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wigfix2bin.pl <wigFixstream> |
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Converts wigFix to a fixed binary format: |
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bytes 00-08 : 'WIGB'<32bit-start-offset> |
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bytes 09... : 2-byte int = value*1000 for each base |
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/; |
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$_=<STDIN>; |
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die("Error: wigFix header not recognized!\n") |
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unless (m/^fixedStep\s/); |
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my ($chr, $cpos)=(m/chrom=(\S+)\s+start=(\d+)/); |
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die("Error: wigFix header not recognized!\n") unless $chr && $cpos; |
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open(BIN, ">$chr.wigfixbin") || die("Error creating file $chr.wigfixbin!\n"); |
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binmode(BIN); |
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print STDERR "Writing $chr.wigfixbin ..\n"; |
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print BIN "WIGB"; |
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print BIN pack('I', $cpos); |
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while (<STDIN>) { |
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if (m/start=(\d+)/) { |
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my $skipto=$1; |
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my $skiplen=$skipto-$cpos; |
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for (my $i=0;$i<$skiplen;$i++) { |
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print BIN pack('s',0); |
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} |
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$cpos=$skipto; |
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next; |
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} |
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my ($v)=(m/^([\d\.\-]+)$/); |
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die("Error parsing value for line $. : $_\n") unless length($v)>0; |
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my $n=int($v*1000); |
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if ($n>32767 || $n<-32767) { |
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die("Error: value out of range ($n)!\n"); |
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} |
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print BIN pack('s',$n); |
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$cpos++; |
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} |
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close(BIN); |
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print STDERR " ..done.\n"; |
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#print STDERR "Waiting for 4s..\n"; |
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#sleep(4); |
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#print STDERR "Now reading data back..\n"; |
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# read back (testing): |
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# open(BIN, "$chr.wigfixbin"); |
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# my ($tag, $r); |
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# read(BIN, $tag, 4); |
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# read(BIN, $r, 4); |
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# my @v=unpack('I',$r); |
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# print STDERR "Header tag=$tag, offset=$v[0]\n"; |
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# while (read(BIN,$r,2)==2) { |
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# @v=unpack('s',$r); |
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# my $n=sprintf('%.3f', $v[0]/1000); |
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# print STDERR "read value: $n\n"; |
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# } |
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# close(BIN); |
