comparison ragoo.pl @ 3:2390a7ae4853 draft

Uploaded

2:fac71ffb07d5

$scaffolds = $sc;

system("cp -rf $scaffolds $tmpdir/scaffolds.fa");
system("cp -rf $reference $tmpdir/reference.fa");
chdir($tmpdir);
system("$dirname/ragoo.py scaffolds.fa reference.fa");


my %hash;
my $id;
open(F,"ragoo_output/ragoo.fasta");

		$hash{$id}.= $_;
	}
}
close(F);

open(O,">$output");
foreach my $id(keys(%hash)){
	print O ">$id\n";
	my $seq = $hash{$id};
	for (my $i =0; $i <= length($seq); $i =$i+80){
		my $subseq = substr($seq,$i,80);

3:2390a7ae4853

$scaffolds = $sc;

system("cp -rf $scaffolds $tmpdir/scaffolds.fa");
system("cp -rf $reference $tmpdir/reference.fa");
chdir($tmpdir);
system("$dirname/ragoo.py scaffolds.fa reference.fa >>$output 2>&1");


my %hash;
my $id;
open(F,"ragoo_output/ragoo.fasta");

		$hash{$id}.= $_;
	}
}
close(F);

open(O,">>$output");
foreach my $id(keys(%hash)){
	print O ">$id\n";
	my $seq = $hash{$id};
	for (my $i =0; $i <= length($seq); $i =$i+80){
		my $subseq = substr($seq,$i,80);