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|
#!/usr/bin/env perl
use strict;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
use Getopt::Std;
use strict;
use Carp;
use Cwd;
use List::Util qw (shuffle);
our ($opt_d, $opt_q, $opt_s, $opt_Q, $opt_b, $opt_p, $opt_O, $opt_h, $opt_c, $opt_B, $opt_X, $opt_M, $opt_S, $opt_o);
&getopts ('dq:s:bp:O:hbc:B:Q:XM:S:o:');
my $usage = <<_EOH_;
############################# Options ###############################
#
# Required:
# -q query multiFastaFile (full or relative path)
# -p program command line template: eg. "/path/to/prog [opts] __QUERY_FILE__ [other opts]"
# -o outdir
#
# Optional:
# -S number of fasta seqs per job submission (default: 1)
# -B bin size (input seqs per directory) (default 5000)
#
###################### Process Args and Options #####################
_EOH_
;
if ($opt_h) {
die $usage;
}
my $CMDS_ONLY = $opt_X;
my $bin_size = $opt_B || 5000;
our $DEBUG = $opt_d;
my $num_seqs_per_job = $opt_S || 1;
unless ($opt_q && $opt_p && $opt_o) {
die $usage;
}
my $queryFile = $opt_q;
unless ($queryFile =~ /^\//) {
$queryFile = cwd() . "/$queryFile";
}
my $program_cmd_template = $opt_p;
unless ($program_cmd_template =~ /__QUERY_FILE__/) {
die "Error, program cmd template must include '__QUERY_FILE__' placeholder in the command";
}
my $out_dir = $opt_o;
## Create files to search
my $fastaReader = new Fasta_reader($queryFile);
my @searchFileList;
my $count = 0;
my $current_bin = 1;
mkdir $out_dir or die "Error, cannot mkdir $out_dir";
my $bindir = "$out_dir/grp_" . sprintf ("%04d", $current_bin);
mkdir ($bindir) or die "Error, cannot mkdir $bindir";
while (my $fastaSet = &get_next_fasta_entries($fastaReader, $num_seqs_per_job) ) {
$count++;
my $filename = "$bindir/$count.fa";
push (@searchFileList, $filename);
open (TMP, ">$filename") or die "Can't create file ($filename)\n";
print TMP $fastaSet;
close TMP;
chmod (0666, $filename);
if ($count % $bin_size == 0) {
# make a new bin:
$current_bin++;
$bindir = "$out_dir/grp_" . sprintf ("%04d", $current_bin);
mkdir ($bindir) or die "Error, cannot mkdir $bindir";
}
}
my $numFiles = @searchFileList;
my $curr_dir = cwd;
if ($numFiles) {
my @cmds;
## formulate blast commands:
foreach my $searchFile (@searchFileList) {
$searchFile = "$curr_dir/$searchFile";
my $cmd = $program_cmd_template;
$cmd =~ s/__QUERY_FILE__/$searchFile/g;
$cmd .= " > $searchFile.OUT ";
$cmd .= " 2>$searchFile.ERR";
push (@cmds, $cmd);
}
@cmds = shuffle(@cmds);
open (my $fh, ">$out_dir.cmds.list") or die $!;
foreach my $cmd (@cmds) {
print $fh "$cmd\n";
}
close $fh;
print STDERR "\n\nCommands written to: $out_dir.cmds.list\n\n";
}
exit(0);
####
sub get_next_fasta_entries {
my ($fastaReader, $num_seqs) = @_;
my $fasta_entries_txt = "";
for (1..$num_seqs) {
my $seq_obj = $fastaReader->next();
unless ($seq_obj) {
last;
}
my $entry_txt = $seq_obj->get_FASTA_format();
$fasta_entries_txt .= $entry_txt;
}
return($fasta_entries_txt);
}
|
