- #!/usr/bin/perl
- use strict;
- use warnings;
- use threads;
- use Thread::Semaphore;
- my $max_thread = 5;
- my $semaphore = Thread::Semaphore->new($max_thread);
- sub TestFun
- {
- $semaphore->up();
- }
- for(my $index = 1; $index <= 10; $index ++)
- {
- $semaphore->down();
- my $thread = threads->create(\&TestFun);
- $thread->detach();
- }
- WaitQuit();
- <pre name="code" class="plain">sub WaitQuit
- {
- my $num = 0;
- while($num < $max_thread)
- {
- $semaphore->down();
- $num ++;
- }
- }
- #!perl
- use warnings;
- use strict;
- use threads;
- use Thread::Semaphore;
- die "perl $0 <thread> <blastConfig> <pep || dna>
- perl $0 3 blast.config dna\n" if @ARGV != 3;
- my $max_thread = $ARGV[0];
- my $semaphore = Thread::Semaphore->new($max_thread);
- mkdir "compliantFasta";
- chdir "compliantFasta";
- open FA, "../$ARGV[1]" or die $!;
- while(<FA>)
- {
- chomp;
- my @tmp = split;
- $semaphore->down();
- my $thread = threads->create(\&adjust, $tmp[0], $tmp[1]);
- $thread->detach();
- }
- &wait;
- chdir "..";
- my $len = 0;
- my ($type, $p);
- if($ARGV[2] =~ /dna/i)
- {
- $len = 30;
- $type = "F";
- $p = "blastn";
- }elsif($ARGV[2] =~ /pep/i){
- $len = 10;
- $type = "T";
- $p = "blastp";
- }
- `orthomclFilterFasta compliantFasta $len 20`;
- `formatdb -i goodProteins.fasta -p $type`;
- mkdir "splitBlast";
- `perl split_fasta.pl goodProteins.fasta 8 splitBlast/blast`;
- my @blast = `ls splitBlast/*`;
- my $sp2 = Thread::Semaphore->new(8);
- foreach my $i(@blast)
- {
- chomp($i);
- $sp2->down();
- my $thread = threads->create(\&blast, $i, $p, $ARGV[0]);
- $thread->detach();
- }
- &wait2;
- `cat splitBlast/*.out > all.blast`;
- `orthomclBlastParser all.blast compliantFasta > similarSequences.txt`;
- `rm all.blast -rf`;
- sub blast
- {
- my ($f, $t, $p) = @_;
- `blastall -p $t -i $f -d goodProteins.fasta -m 8 -F F -b 1000 -v 1000 -a $p -o $f.out`;
- $sp2->up();
- }
- sub wait2
- {
- my $num = 0;
- while($num < 8)
- {
- $sp2->down();
- $num ++;
- }
- }
- sub adjust
- {
- my ($label, $path) = @_;
- `orthomclAdjustFasta $label $path 1`;
- $semaphore->up();
- }
- sub wait
- {
- my $num = 0;
- while($num < $max_thread)
- {
- $semaphore->down();
- $num ++;
- }
- }