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run_motif_family.pl
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#!/usr/bin/perl
my $teiserdir ;
BEGIN{
if ((!$ENV{TEISERDIR}) || ($ENV{TEISERDIR} eq '')) {
$teiserdir="./" ;
print "The TEISERDIR environment variable is not set. It is set to default.\n";
}
else{
print "The TEISERDIR environment variable is ".$ENV{TEISERDIR}."\n" ;
$teiserdir = $ENV{TEISERDIR};
}
}
my $cmdline = "perl teiser.pl";
foreach my $r (@ARGV) {
$cmdline .= " $r";
}
my $programdir = $teiserdir."/Programs" ;
my $scriptdir = $teiserdir."/Scripts" ;
my $pwd = `pwd`; $pwd =~ s/\n//;
use lib "$teiserdir/Scripts";
use PBS ;
use strict;
use Sets;
use Table;
use Getopt::Long;
use Data::Dumper;
if (@ARGV == 0) {
die "Usage: perl teiser.pl --expfile=FILE --exptype=TXT --species=SP\n";
}
my @argv_copy = @ARGV;
my $expfile = undef ;
my $motiffile = undef ;
my $listfile = undef ;
my $homologyfile = undef ;
my $fastafile_rna = undef ;
my $species = undef ;
my $exptype = "discrete" ;
my $ebins = undef ;
my $quantized = 1 ;
my $divbins = 50.0 ;
my $mbins = 2 ;
my $type = "DN" ;
my $shuffle_mifind = 1500000 ;
my $maxp_mifind = 0.00000001 ;
my $shuffle_mimotif = 1000000 ;
my $maxp_mimotif = 0.0000001 ;
my $shuffle_page = 10000 ;
my $maxp_page = 0.005 ;
my $maxz_mioptimize = -1 ;
my $maxz_mifind = -1 ;
my $jn_t = 8 ;
my $min_r = 2.0 ;
my $dG_t = -1.0 ;
my $clusters = 5 ;
my $draw_min = -10 ;
my $draw_max = 10 ;
my $removecols_draw = undef ;
my $colmap_matrix = "$scriptdir/HEATMAPS/cmap_1.txt" ;
my $colmap_mimatrix = "$scriptdir/HEATMAPS/cmap_2.txt" ;
my $colmap_page = "$scriptdir/HEATMAPS/cmap_3.txt" ;
my $order = 0 ;
my $dodrawmatrix = 1 ;
my $dodrawmimatrix = 1 ;
my $dodrawpagematrix = 1 ;
my $dodrawmotifs = 1 ;
my $doskipdiscovery = 0 ;
my $domifind = 1 ;
my $doskipoptimization = 0 ;
my $domioptimize = 1 ;
my $doonlypositive = 0 ;
my $domireport = 1 ;
my $doremovedups = 1 ;
my $doremoveextras = 1 ;
my $dopagerun = 1 ;
my $domotifind = 1 ;
my $doconservation = 1 ;
my $suffix = "" ;
my $submit = 0 ;
my $platform = undef ;
my $walltime = "72:00:00" ;
my $queue = undef ;
my $jobid = undef ;
GetOptions ('expfile=s' => \$expfile,
'motiffile=s' => \$motiffile,
'fastafile_rna=s' => \$fastafile_rna,
'species=s' => \$species,
'exptype=s' => \$exptype,
'ebins=i' => \$ebins,
'quatized=i' => \$quantized,
'divbins=i' => \$divbins,
'mbins=i' => \$mbins,
'type=s' => \$type,
'shuffle_mifind=i' => \$shuffle_mifind,
'maxp_mifind=f' => \$maxp_mifind,
'shuffle_mimotif=i' => \$shuffle_mimotif,
'maxp_mimotif=f' => \$maxp_mimotif,
'shuffle_page=i' => \$shuffle_page,
'maxp_page=f' => \$maxp_page,
'maxz_mioptimize=f' => \$maxz_mioptimize,
'maxz_mifind=f' => \$maxz_mifind,
'jn_t=i' => \$jn_t,
'min_r=f' => \$min_r,
'dG_t=f' => \$dG_t,
'cluaters=i' => \$clusters,
'order=i' => \$order,
'draw_min=f' => \$draw_min,
'draw_max=f' => \$draw_max,
'removecols_draw=i' => \$removecols_draw,
'dodrawmatrix=i' => \$dodrawmatrix,
'dodrawmimatrix=i' => \$dodrawmimatrix,
'dodrawpagematrix=i' => \$dodrawpagematrix,
'dodrawmotifs=i' => \$dodrawmotifs,
'doskipdiscovery=i' => \$doskipdiscovery,
'doskipoptimization=i' => \$doskipoptimization,
'domifind=i' => \$domifind,
'domioptimize=i' => \$domioptimize,
'doonlypositive=i' => \$doonlypositive,
'domireport=i' => \$domireport,
'doremovedups=i' => \$doremovedups,
'doremoveextras=i' => \$doremoveextras,
'dopagerun=i' => \$dopagerun,
'domotifind=i' => \$domotifind,
'doconservation=i' => \$doconservation,
'suffix=s' => \$suffix,
'submit=i' => \$submit,
'platform=s' => \$platform,
'walltime=s' => \$walltime,) ;
if (!defined($expfile)) {
die("Please input an expression file (--expfile=FILE).\n");
}
if ($doskipdiscovery == 1) {
$domifind = 0;
$domioptimize = 0;
}
if ($doskipoptimization == 1) {
$domioptimize = 0;
}
if ($exptype eq "discrete") {
$quantized = 1 ;
} elsif ($exptype eq "continuous"){
$quantized = 0 ;
}
if (($quantized == 0) && (!defined($removecols_draw))) {
$removecols_draw = 0;
}
if (defined($species)) {
# read species file
my $species_data = readSpeciesData($species);
$fastafile_rna = $species_data->{"fastafile_rna"} if (!defined($fastafile_rna)) ;
$homologyfile = $species_data->{"homologyfile"} if (!defined($homologyfile)) ;
$listfile = $species_data->{"genelistfile"} if (!defined($listfile));
}
my $time = Sets::getNiceDateTime(1) ;
my $a_ref_files = Sets::getFiles($expfile);
foreach my $expfile (@$a_ref_files) {
if (&check_input_file($expfile, $exptype) == 0) {
die "Please correct input expression file.\n";
}
my $expfile_file = Sets::filename($expfile);
my $target_dir = "$expfile"."_FAMILY"."/$suffix";
if ($suffix eq ""){
$target_dir = "$expfile"."_FAMILY";
}
if (! -e "$expfile"."_FAMILY") {
mkdir "$expfile"."_FAMILY" ;
}
if (! -e $target_dir) {
mkdir $target_dir;
}
open OUTC, ">$target_dir/cmdline.txt"
or print "Cannot open $target_dir/cmdline.txt";
print OUTC "$cmdline\n";
close OUTC;
######## remove duplicates ########
my $expfile_nodups = "$target_dir/$expfile_file" ;
my $expfile_pre = "$target_dir/$expfile_file.pre" ;
my $pbs = PBS->new;
$pbs->setPlatform($platform) if (defined($platform));
$pbs->setQueue($queue) if (defined($queue));
$pbs->setWallTime($walltime);
$pbs->addCmd("export TEISERDIR=$teiserdir");
$pbs->addCmd("cd $pwd");
$pbs->setScriptName("$target_dir/$expfile_file.script");
$pbs->addCmd("date");
if ($doremoveextras == 1) {
$pbs->addCmd("echo \"Remove genes without sequence info, create $target_dir/$expfile_pre\"");
$pbs->addCmd("perl $scriptdir/remove_genes_without_sequence.pl --expfile=$expfile --listfile=$listfile --outfile=$expfile_pre");
}else{
system("cp $expfile $expfile_pre") ;
}
$pbs->addCmd("echo \"Remove duplicates, create $target_dir/$expfile_file\"");
if ($doremovedups == 1) {
my %PARAMS = ("expfile" => $expfile_pre,
"quantized" => $quantized,
"fastafile" => $fastafile_rna,
"dupfile" => undef,
"ebins" => $ebins,
"divbins" => $divbins,
"outfile" => $expfile_nodups) ;
my $cmd = &get_cmd_removedups(\%PARAMS) ;
$pbs->addCmd($cmd) ;
}else{
system("cp $expfile_pre $expfile_nodups") ;
}
######## quatize expression profile ########
my $expfile_quant = "$target_dir/$expfile_file.q" ;
if ($quantized == 0) {
$pbs->addCmd("echo \"Quantizing the input file.\"");
my $cmd = "perl $scriptdir/quantize_input_vector.pl --expfile=$expfile_nodups --outfile=$expfile_quant";
if (defined($ebins)) {
$cmd .= " -ebins $ebins ";
}
if (defined($divbins)) {
$cmd .= " -divbins $divbins ";
}
$pbs->addCmd($cmd);
}
######## mi report for motif family ########
my $matrixfile = "$target_dir/$expfile_file.fmatrix" ;
my $summaryfile = "$target_dir/$expfile_file.fsummary" ;
my $reportfile = "$target_dir/$expfile_file.freport" ;
my $profile = "$target_dir/$expfile_file.fprofile" ;
$pbs->addCmd("echo \"step 2: mi report for motif family.\"");
my %PARAMS = ("expfile" => $expfile_nodups,
"quantized" => $quantized,
"shuffle" => $shuffle_mifind,
"rna_fastafile" => $fastafile_rna,
"motiffile" => $motiffile,
"ebins" => $ebins,
"divbins" => $divbins,
"minr" => $min_r,
"matrixfile" => $matrixfile,
"summaryfile" => $summaryfile,
"reportfile" => $reportfile,
"profile" => $profile,
"max_p" => $maxp_mifind,
"max_z" => $maxz_mioptimize) ;
my $cmd = &get_cmd_mi_report_motif_family(\%PARAMS);
$pbs->addCmd($cmd);
######## RNA fold ########
my $cmd = "perl -pi -e 's/\\t/_/g' $reportfile";
$pbs->addCmd($cmd);
$pbs->addCmd("echo \"step 3: Running Vienna RNAfold.\"");
$pbs->addCmd($cmd);
my $cmd = "/Users/hani/Life/Projects/Applications/ViennaRNA-2.1.2/Progs/RNAfold -p0 --noPS < $reportfile > $reportfile.vienna";
$pbs->addCmd($cmd);
my $cmd = "perl $scriptdir/decode_vienna_by_motif_match.pl $reportfile.vienna > $reportfile.vienna.parsed" ;
$pbs->addCmd($cmd);
my $cmd = "cut -f 5 $reportfile.vienna.parsed > $reportfile.vienna.parsed.dG" ;
$pbs->addCmd($cmd);
my $cmd = "AVE=\$(cat $reportfile.vienna.parsed.dG ".'| perl -e \'use List::Util qw(max min sum); @a=();while(<>){$sqsum+=$_*$_; push(@a,$_)}; $n=@a;$s=sum(@a);$a=$s/@a;$m=max(@a);$mm=min(@a);$std=sqrt($sqsum/$n-($s/$n)*($s/$n));$mid=int @a/2;@srtd=sort @a;if(@a%2){$med=$srtd[$mid];}else{$med=($srtd[$mid-1]+$srtd[$mid])/2;};print $a;\')' ;
$pbs->addCmd($cmd);
my $cmd = "SD=\$(cat $reportfile.vienna.parsed.dG ".'| perl -e \'use List::Util qw(max min sum); @a=();while(<>){$sqsum+=$_*$_; push(@a,$_)}; $n=@a;$s=sum(@a);$a=$s/@a;$m=max(@a);$mm=min(@a);$std=sqrt($sqsum/$n-($s/$n)*($s/$n));$mid=int @a/2;@srtd=sort @a;if(@a%2){$med=$srtd[$mid];}else{$med=($srtd[$mid-1]+$srtd[$mid])/2;};print $std;\')' ;
$pbs->addCmd($cmd);
my $cmd = 'THRESH=$(($AVE - $SD))' ;
$pbs->addCmd($cmd);
my $cmd = 'awk -v t=$THRESH \'{if ($5<t) print}\''." $reportfile.vienna.parsed > $reportfile.vienna.parsed.selected" ;
$pbs->addCmd($cmd);
my $cmd = "cut -f 2 $reportfile.vienna.parsed.selected | sort -u > $reportfile.vienna.parsed.selected.list" ;
$pbs->addCmd($cmd);
######## mi report for gene list ########
my $genefile = "$reportfile.vienna.parsed.selected.list" ;
my $matrixfile = "$target_dir/$expfile_file.matrix" ;
my $summaryfile = "$target_dir/$expfile_file.summary" ;
my $reportfile = "$target_dir/$expfile_file.report" ;
my $profile = "$target_dir/$expfile_file.profile" ;
$pbs->addCmd("echo \"step 4: mi report for gene list.\"");
my %PARAMS = ("expfile" => $expfile_nodups,
"quantized" => $quantized,
"shuffle" => $shuffle_mifind,
"genefile" => $genefile,
"ebins" => $ebins,
"divbins" => $divbins,
"minr" => $min_r,
"matrixfile" => $matrixfile,
"summaryfile" => $summaryfile,
"reportfile" => $reportfile,
"profile" => $profile,
"max_p" => $maxp_mifind,
"max_z" => $maxz_mioptimize) ;
my $cmd = &get_cmd_mi_report_gene_list(\%PARAMS);
$pbs->addCmd($cmd);
######## drawing matrix ########
if ($dodrawmatrix == 1){
$pbs->addCmd("echo \"step 7: drawing matrix.\"");
my %PARAMS = ("pvmatrixfile" => $matrixfile,
"summaryfile" => $summaryfile,
"expfile" => $expfile_nodups,
"quantized" => $quantized,
"colmap" => $colmap_matrix,
"order" => $order,
"min" => $draw_min,
"max" => $draw_max,
"cluster" => $clusters,
"suffix" => "",) ;
my $cmd = &get_cmd_drawmatrix(\%PARAMS);
$pbs->addCmd($cmd);
}
if ($submit == 0) {
$pbs->execute;
}else{
$jobid = $pbs->submit; print "Submitted job $jobid.\n";
}
}
sub readSpeciesData {
my ($species) = @_;
my %H = ();
open IN, "$ENV{TEISERDIR}/TEISER_Data/species_data/$species" or die "No data file for $species.\n";
while (my $l = <IN>) {
chomp $l;
my @a = split /\t/, $l, -1;
if ($a[1] =~ /^TEISER_Data/) {
$a[1] = "$ENV{TEISERDIR}/$a[1]";
}
$H{$a[0]} = $a[1];
}
close IN;
return \%H;
}
sub check_input_file {
my ($expfile, $exptype) = @_;
my $ta = Table->new;
$ta->loadFile($expfile);
my $a_ref = $ta->getArray();
my $r = shift @$a_ref;
if ($r->[1] =~ /^\d/) {
print "WARNING: your file might not contain a header line ($r->[1]).\n";
}
if (scalar(@$a_ref)<2){
print "ERROR: your expfile is not valid. Most probably it contains '\r' instead of '\n'\n" ;
return 1 ;
}
my %H = ();
my %V = ();
foreach my $r (@$a_ref) {
if (defined($H{$r->[0]})) {
print "Your files contains multiple rows with the same gene id. Please correct that before applying TEISER.\n";
return 0;
}
$H{$r->[0]} ++;
$V{$r->[1]} = 1;
}
my @v = values ( %V );
@v = sort { $a <=> $b } @v;
my $max = $#v;
if (($exptype eq 'discrete') && (scalar(@v) != $max+1)) {
my $n1 = scalar(@v);
my $n2 = $max + 1;
die "Problem. Your discrete vector is missing some symbols ($n1 != $n2).\n";
return 0;
}
return 1;
}
sub get_cmd_removedups {
my ($p) = @_;
my $todo = "perl $scriptdir/remove_duplicates.pl --expfile=$p->{expfile} --quantized=$p->{quantized} --fastafile=$p->{fastafile} --outfile=$p->{outfile}";
if (defined($p->{dupfile})) {
$todo .= " --dupfile=$p->{dupfile} ";
}
if (defined($p->{ebins})) {
$todo .= " --ebins=$p->{ebins} ";
}
if (defined($p->{divbins})) {
$todo .= " --divbins=$p->{divbins} ";
}
return $todo;
}
sub get_cmd_mi_report_motif_family {
my ($p) = @_;
my $todo = "$programdir/mi_report_motif_family -expfile $p->{expfile} -motiffile $p->{motiffile} -rna_fastafile $p->{rna_fastafile} -reportfile $p->{reportfile} -matrixfile $p->{matrixfile} -summaryfile $p->{summaryfile} -profile $p->{profile} -quantized $p->{quantized} -shuffle $p->{shuffle}" ;
if (defined($p->{ebins})) {
$todo .= " -ebins $p->{ebins} ";
}
if (defined($p->{divbins})) {
$todo .= " -divbins $p->{divbins} ";
}
return $todo;
}
sub get_cmd_mi_report_gene_list {
my ($p) = @_;
my $todo = "$programdir/mi_report_gene_list -expfile $p->{expfile} -genefile $p->{genefile} -quantized $p->{quantized} -shuffle $p->{shuffle} -matrixfile $p->{matrixfile} -summaryfile $p->{summaryfile} -profile $p->{profile}" ;
if (defined($p->{ebins})) {
$todo .= " -ebins $p->{ebins} ";
}
if (defined($p->{jn_t})) {
$todo .= " -jn_t $p->{jn_t} ";
}
if (defined($p->{divbins})) {
$todo .= " -divbins $p->{divbins} ";
}
return $todo;
}
sub get_cmd_drawmatrix {
my ($p) = @_;
my $todo = "perl $scriptdir/teiser_draw_matrix.pl --pvmatrixfile=$p->{pvmatrixfile} --summaryfile=$p->{summaryfile} --expfile=$p->{expfile} --quantized=$p->{quantized} --colmap=$p->{colmap} --order=$p->{order} --min=$p->{min} --max=$p->{max} --cluster=$p->{cluster} --suffix=$p->{suffix}" ;
return $todo;
}