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#!/usr/bin/perl
#
# createAugustusJoblist.pl
# Create a joblist with overlapping sequence chunks from multiple fasta files.
# Mario Stanke, 22.01.2007
#
#
use strict;
use Getopt::Long;
my $usage = "$0 -- Create a joblist with sequence chunks from multiple fasta files.\n\n";
$usage .= "Usage: $0\n\n";
$usage .= "parameters:\n";
$usage .= "--sequences seqs.lst input sequences, format: each line contains one sequence including the full path and its size, e.g.\n";
$usage .= " /cluster/data/panTro2/1/chr1.fa\t1\t229974691\n";
$usage .= " /cluster/data/panTro2/1/chr1_random\t1\t9420409\n";
$usage .= " /cluster/data/panTro2/2/chr2a\t1\t114460064\n";
$usage .= " or\n";
$usage .= " /cluster/data/panTro2/1/chr1_random\t/hints/chr1_random\t1\t9420409\n";
$usage .= " /cluster/data/panTro2/2/chr2a\t/hints/chr2a\t1\t114460064\n";
$usage .= "--outputdir s directory, in which later the AUGUSTUS output will be written.\n";
$usage .= "--command s AUGUSTUS command, e.g. \"augustus --species=human --maxDNAPieceSize=600000\".\n";
$usage .= "--joblist job.lst filename with list of jobs as given to parasol.\n";
$usage .= "--chunksize n chunk size. Each sequence is (imaginarily) cut into chunks of this size\n\n";
$usage .= "options:\n";
$usage .= "--overlap n overlap. Neighboring chunks overlap by this number of bases.\n";
$usage .= "--padding n padding on both sides (default 0).\n";
$usage .= "--errordir errdir directory, in which later the AUGUSTUS error messages will be written.\n";
$usage .= "--check insert parasol input/output checks.\n";
$usage .= "--wrap=s have each job in a separate file, preceded by command s.\n";
$usage .= "--jobprefix=s prefix of job name (default: \"job.\")\n";
if (@ARGV < 2) {
print $usage;
exit;
}
my ($seqfilename, $chunksize, $overlap, $outputdir, $errordir, $command, $joblist, $seqnr, $name, $predStart, $predEnd, $pE, $chunkid, $padding, $check, $wrap, $wholecommand);
my $jobnr = 0;
$padding = 0;
$check = 0;
$wrap = "";
my $jobprefix = "job.";
GetOptions('sequences=s'=>\$seqfilename,
'chunksize=i'=>\$chunksize,
'overlap:i'=>\$overlap,
'outputdir=s'=>\$outputdir,
'errordir=s'=>\$errordir,
'command=s'=>\$command,
'padding:i'=>\$padding,
'joblist=s'=>\$joblist,
'check!'=>\$check,
'wrap=s'=>\$wrap,
'jobprefix:s'=>\$jobprefix);
die ("Need to specify chunksize.\n") unless (defined $chunksize);
die ("Need to specify command.\n") unless (defined $command);
die ("Need to specify joblist.\n") unless (defined $joblist);
die ("Need to specify chunksize.\n") unless (defined $chunksize);
die ("Need to specify outputdir.\n") unless (defined $outputdir);
open(SEQ, "<$seqfilename") or die ("Could not open $seqfilename");
open (BATCH, ">$joblist") or die "Couldn't open $joblist\n";
$outputdir =~ s/\/$//;
$seqnr = 1;
while (<SEQ>) {
my ($path, $start, $end, $hints);
if (/(.+)\s+(.+)\s+(.+)\s+(.+)/) {
$path = $1;
$hints = $2;
$start = $3;
$end = $4;
} elsif (/(.+)\s+(.+)\s+(.+)/){
$path = $1;
$start = $2;
$end = $3;
undef $hints;
}
$start -= $padding;
$end += $padding;
my $ovlp;
if (!$overlap) {
$ovlp = (($chunksize > 3000000)? 500000 : $$chunksize/6);
} else {
$ovlp = $overlap;
}
my $chunknr = 0;
$name = $path;
$name =~ s/.*\///;
$predEnd = -1;
for ($predStart = $start; $predStart <= $end && $predEnd < $end; $predStart = $predEnd+1-$ovlp) {
$chunknr++;
$predEnd = $predStart + $chunksize-1;
$pE = $predEnd;
if ($pE > $end){
$pE = $end;
}
$chunkid = sprintf ("%03d", $chunknr);
my $gfffilename = "$outputdir/$seqnr.$chunkid.${name}.$predStart..$pE.gff";
my $errorfilename;
if (defined $errordir) {
$errorfilename = "$errordir/$seqnr.$chunkid.${name}.$predStart..$predEnd.err";
} else {
$errorfilename = "$outputdir/$seqnr.$chunkid.${name}.$predStart..$pE.err";
}
$wholecommand = $command;
if (defined $hints) {
if ($check){
$wholecommand .= " --hintsfile={check in exists $hints}";
} else {
$wholecommand .= " --hintsfile=$hints";
}
}
if ($check) {
$wholecommand .= " --predictionStart=$predStart --predictionEnd=$pE {check in line+ $path} --outfile={check out line+ $gfffilename} --errfile=$errorfilename\n";
} else {
$wholecommand .= " --predictionStart=$predStart --predictionEnd=$pE $path --outfile=$gfffilename --errfile=$errorfilename\n";
}
if ($wrap eq "") {
print BATCH $wholecommand;
} else {
$jobnr++;
my $jobname = "$jobprefix$jobnr";
open (JOB, ">$jobname");
print JOB "$wrap\n" . $wholecommand;
print BATCH "$jobname\n";
close JOB;
system("chmod +x $jobname");
}
}
$seqnr++;
}
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