/usr/bin/aln2bed is in art-nextgen-simulation-tools 20160605+dfsg-2build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | #!/usr/bin/perl
#convert Aln format to the UCSC BED format
#weichun huang at whduke@gmail.com
use strict;
my @alnFile=@ARGV;
if(@ARGV<2){
print "aln2bed converts ALN files to a BED file\n\n";
print "USAGE: ";
print "aln2bed out_bed_file.bed in_aln_file_1 [ in_aln_file_2 ...]\n\n";
exit(1);
}
my $score=500; #all scores are 500.
#bed file: ref_id st_pos end_pos read_id 500 strand
my $bedFile=shift @alnFile;
open(BED, ">$bedFile") or die $!;
my %reflen;
foreach my $af (@alnFile){
open(ALN, "<$af") or die $!;
my $i=0;
#read header
while (<ALN>){
chomp;
if($i==0){
if(!/^##ART/){
print STDERR "File $af is not an ART ALN file.\n Exit ...\n";
exit(1);
}
$i=1;
}
elsif(/^\@SQ\t(\S+)\t(\d+)/){
$reflen{"$1"}=$2;
}
elsif(/^\@CM/){
next;
}
elsif(/^##Header\s+End/){
last;
}
}
#read aln records
while (<ALN>){
chomp;
if(s/^>//){
my ($ref_id, $read_id, $st_pos, $strand)=split /\t/;
my $len=0;
while (<ALN>){
chomp;
if(/^\w/){
s/-//g;
$len=length; #lenth of reference part
}
last;
}
if($strand eq "+"){
printf BED "%s\t%d\t%d\t%s\t%d\t%s\n", ($ref_id, $st_pos, $st_pos+$len, $read_id, $score, $strand);
}
else{
my $stop=$reflen{$ref_id}-$st_pos;
printf BED "%s\t%d\t%d\t%s\t%d\t%s\n", ($ref_id, $stop-$len, $stop, $read_id, $score, $strand);
}
}
}
}
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