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#!/usr/bin/perl
#
# createAugustusJoblist.pl
# Create a joblist with overlapping sequence chunks from multiple fasta files.
#
# This script is used by the braker.pl pipeline.
# Please be extremely careful when changing this script because the braker.pl
# pipeline may fail upon custom modification of this script.
# In case of doubt, contact katharina.hoff@uni-greifswald.de
#
# Mario Stanke & Katharina J. Hoff, last changes on Dec 6 2021
#
#
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";
$usage .= "--partitionHints partition hints files according to genomic locus of single augustus runs,\n";
$usage .= " add a command to the augustus job that will create and delete this hints file\n";
$usage .= " in the output directory of the augustus job. This option also will automatically\n";
$usage .= " delete empty error files of augustus.\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, $partitionHints, $localHints
);
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,
'partitionHints!' => \$partitionHints
);
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..$pE.gff";
if($gfffilename=~m/\;/){
$gfffilename=s/\;/\\\;/;
}
my $errorfilename;
if($errorfilename=~m/\;/){
$errorfilename=~s/\;/\\\;/;
}
if ( defined $errordir ) {
$errorfilename = "$errordir/$seqnr.$chunkid.${name}.$predStart..$pE.err";
}
else {
$errorfilename = "$outputdir/$seqnr.$chunkid.${name}.$predStart..$pE.err";
}
$wholecommand = "";
if( $partitionHints ) {
$localHints = "$outputdir/$seqnr.$chunkid.${name}.$predStart..$pE.hints";
if($localHints=~m/\;/){
$localHints=~s/\;/\\\;/;
}
my $locus = ${name};
$locus =~ s/(.*)\..*/$1/;
$wholecommand .= "grep \"^$locus\" $hints | awk ' {if (\$4 >= $predStart ) print \$0 } ' | awk ' {if (\$5 <= $pE) print \$0 } ' > $localHints\n";
} else {
$localHints = $hints;
}
$wholecommand .= $command;
if ( defined $hints ) {
if ($check) {
$wholecommand .= " --hintsfile={check in exists $localHints}";
}
else {
$wholecommand .= " --hintsfile=$localHints";
}
}
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( $partitionHints ) {
$wholecommand .= "if [ -e $outputdir/$seqnr.$chunkid.${name}.$start..$end.hints ]\nthen\nrm $outputdir/$seqnr.$chunkid.${name}.$start..$end.hints\nfi\n";
# for braker.pl (where we use partitionHints) I want to delete empty error files
$wholecommand .= "if [ ! -s $errorfilename ]; then rm -f $errorfilename;fi\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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