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|
#!/usr/bin/perl -w
use strict;
my $mm=-M "$ENV{srcdir}/.done";
exit 0 if (-e "$ENV{srcdir}/.done" && (-M "$ENV{srcdir}/generate_data.pl" > -M "$ENV{srcdir}/.done"));
my $seed = 15551;
sub rr {
my ($m)=@_;
$seed = int(($seed*1103515245+12345)&0xffffffff);
if (defined($m)) {
return $seed % $m;
} else {
return ($seed & 0xffffff) / 0x1000000;
}
}
# Loads a fasta file into a hash
sub load_fasta {
my ($fn) = @_;
my %seqs;
open(my $fd, "<", $fn) || die "$fn: $!\n";
my $name = undef;
my $s = "";
while (<$fd>) {
chomp($_);
if (/^>(\S+)/) {
if (defined($name)) {
$seqs{$name} = $s;
}
$name = $1;
$s = "";
} else {
$s .= $_;
}
}
$seqs{$name} = $s;
close($fd);
return \%seqs;
}
#---- Load seq
print "Loading ce.fa\n";
my $seqs = load_fasta("$ENV{srcdir}/data/ce.fa");
my @names = keys(%$seqs);
my %len;
my $n;
my @base = qw/A C G T/;
if (! -w "$ENV{srcdir}/data") {
chmod(0755, "$ENV{srcdir}/data") || die "$ENV{srcdir}/data: $!";
chmod(0755, "$ENV{srcdir}") || die "$ENV{srcdir}: $!";
}
#---- Generate sorted data
print "Generating ce#sorted.sam\n";
open(my $out, ">", "$ENV{srcdir}/data/ce#sorted.sam") ||
die "$ENV{srcdir}/data/ce#sorted.sam: $!";
# Create @SQ headers
foreach (sort @names) {
my $len = length($seqs->{$_});
print $out "\@SQ\tSN:$_\tLN:$len\n";
$len{$_} = $len;
}
# Sequence lines
$n = 1;
$len{"*"}=$len{$names[0]};
$seqs->{"*"}=$seqs->{$names[0]};
foreach my $chr ((sort @names),"*") {
my $len = $len{$chr};
my $s = $seqs->{$chr};
for (my $i=0; $i<$len-100; $i++) {
if (rr() < 0.1) { #10x coverage
my $dna = substr($s,$i,100);
$dna = substr($s, int(rr($len{"*"}-100)), 100) if ($chr eq "*");
for (my $j=0; $j<5; $j++) {
substr($dna, 100*rr(), 1) = $base[4*rr()];
}
if ($chr eq "*") {
print $out "Seq",$n++,"\t4\t$chr\t0\t0\t*\t*\t0\t0\t$dna\t*\n";
} else {
print $out "Seq",$n++,"\t0\t$chr\t",$i+1,"\t2\t100M\t*\t0\t0\t$dna\t*\n";
}
}
}
}
close($out) || die;
#---- Generate unsorted data
print "Generating ce#unsorted.sam\n";
srand 15551;
open($out, ">", "$ENV{srcdir}/data/ce#unsorted.sam") ||
die "$ENV{srcdir}/data/ce#unsorted.sam: $!";
# Create @SQ headers
foreach (sort @names) {
my $len = length($seqs->{$_});
print $out "\@SQ\tSN:$_\tLN:$len\n";
$len{$_} = $len;
}
# Sequence lines
$n = 1;
for (my $i = 0; $i < 100000; $i++) {
my $chr = $names[$#names*rr()];
my $pos = int(rr() * ($len{$chr}-100));
my $dna = substr($seqs->{$chr},$pos,100);
for (my $j=0; $j<5; $j++) {
substr($dna, 100*rr(), 1) = $base[4*rr()];
}
print $out "Seq",$n++,"\t0\t$chr\t",$pos+1,"\t2\t100M\t*\t0\t0\t$dna\t*\n";
}
close($out) || die;
#---- Tidy up
open(DONE, ">$ENV{srcdir}/.done")||die;
close(DONE);
|
