multiT_runLastal.pl

#!/usr/bin/perl -w

use threads;
use threads::shared; 

die "Usage: perl $0 query.fasta database.fasta threads identity out.aln\n" 
if(!defined($ARGV[0]) || !defined($ARGV[1]) || !defined($ARGV[2]) || !defined($ARGV[4]));

my $query      = $ARGV[0];
my $dataB      = $ARGV[1];
my $maxThreads = int $ARGV[2]/2;
my $identity   = (defined $ARGV[3])?$ARGV[3]:60;
my $outaln     = $ARGV[4];
system("rm -rf faByChr");
system("mkdir faByChr");
system("rm -rf tmp");
system("mkdir tmp");
#system("rm dblast*");
#system("lastdb -uNEAR -R01 dblast $dataB");

my %infordb;
my %namedb;
my $count = 0;
open(IN, $query) or die"";
$/='>';
<IN>;
while(<IN>){
	chomp;
	my ($name,$seq) = split(/\n/,$_,2);
	$name  =~ s/\s+.*//g;
	$seq   =~ s/\s+//g;
	$count++;
	$infordb{$count}->{'name'}  = $name;
	$infordb{$count}->{'seq'}   = $seq;
	my $rname       = $count;	
  $namedb{$rname} = $name;
  $infordb{$count}->{'rname'} = $rname;
  my $outfile     = $rname.".fasta";
	open(my $out, ">faByChr/$outfile") or die"";
	print $out ">$rname\n$seq\n";
	close $out;	

	}
close IN;

system("rm command.txt");
system("ls faByChr/*fasta |xargs -I\{\} basename \{\} .fasta|xargs -I\{\} echo \"lastal -P 1 dblast faByChr/{}.fasta -a 180 -b 1 -q 80 -r 30|maf-convert blasttab  >tmp/\{\}.out\" >>command.txt");
system("ParaFly -c command.txt -CPU $maxThreads");

open(OUT, "> $outaln") or die"";
open(IN, "cat tmp/*.out |awk '\$3>88' |") or die"";
my $content = <IN>;
@linedb = split(/\n/,$content);
foreach my $line (@linedb){
	my @data = split(/\s+/,$line);
	$data[0] = $namedb{$data[0]} if(exists($namedb{$data[0]}));
	foreach my $i(0..$#data){
		print OUT "$data[$i]	";
		}
	print OUT "\n";
	}
close IN;
close OUT;
system("rm -rf tmp/");

#sub run_lastal{
#  my $scaf = shift;
#  my $cmd  = "lastal -P 2 dblast faByChr/".$scaf.".fasta -a 180 -b 1 -q 80 -r 30 |maf-convert blasttab |awk '\$3>$identity' > tmp/".$scaf.".out";
#  system($cmd);	
#	}