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|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib ("$FindBin::Bin/../PerlLib");
use Pipeliner;
my $utildir = "$FindBin::Bin/PWM";
my $help_flag;
my $pwm_left = 20;
my $pwm_right = 10;
my $usage = <<__EOUSAGE__;
####################################################################
#
# --transcripts <string> target transcripts fasta file
#
# --selected_orfs <string> longest_orfs.cds.top_longest_5000.nr80
#
# --out_prefix <string> output prefix
#
# Optional:
#
# --pwm_left <int> default: $pwm_left
#
# --pwm_right <int> default: $pwm_right
#
#
#####################################################################
__EOUSAGE__
;
my $transcripts_file;
my $selected_orfs_file;
my $out_prefix;
&GetOptions ( 'help|h' => \$help_flag,
'transcripts=s' => \$transcripts_file,
'selected_orfs=s' => \$selected_orfs_file,
'pwm_left=i' => \$pwm_left,
'pwm_right=i' => \$pwm_right,
'out_prefix=s' => \$out_prefix,
);
if ($help_flag) {
die $usage;
}
unless ($transcripts_file && $selected_orfs_file && $out_prefix) {
die $usage;
}
main: {
my $checkpoints_dir = "${out_prefix}_" . time() . "_checkpoints";
if (! -d $checkpoints_dir) {
mkdir($checkpoints_dir) or die $!;
}
my $pipeliner = new Pipeliner(-verbose => 2, -checkpoint_dir => $checkpoints_dir);
my $cmd = "$utildir/build_atgPWM_+-.pl "
. " --transcripts $transcripts_file "
. " --selected_orfs $selected_orfs_file "
. " --out_prefix $out_prefix"
. " --pwm_left $pwm_left --pwm_right $pwm_right ";
$pipeliner->add_commands(new Command($cmd, "built_init.ok"));
$cmd = "$utildir/feature_scoring.+-.pl "
. " --features_plus $out_prefix.+.features "
. " --features_minus $out_prefix.-.features "
. " --atg_position $pwm_left "
. " > $out_prefix.feature.scores";
$pipeliner->add_commands(new Command($cmd, "score_features.ok"));
$cmd = "$utildir/feature_scores_to_ROC.pl $out_prefix.feature.scores > $out_prefix.feature.scores.roc";
$pipeliner->add_commands(new Command($cmd, "roc_features.ok"));
$cmd = "$utildir/plot_ROC.Rscript $out_prefix.feature.scores.roc || :";
$pipeliner->add_commands(new Command($cmd, "rocplot.ok"));
$cmd = "$utildir/compute_AUC.pl $out_prefix.feature.scores.roc";
$pipeliner->add_commands(new Command($cmd, "aucplot.ok"));
$cmd = "$utildir/make_seqLogo.Rscript $out_prefix.+.pwm || :";
$pipeliner->add_commands(new Command($cmd, "seqlogo.+.ok"));
$cmd = "$utildir/make_seqLogo.Rscript $out_prefix.-.pwm || :";
$pipeliner->add_commands(new Command($cmd, "seqlogo.-.ok"));
#################
## motif enhancer
$cmd = "$utildir/deplete_feature_noise.pl "
. " --features_plus $out_prefix.+.features "
. " --pwm_minus $out_prefix.-.pwm "
. " --out_prefix $out_prefix.enhanced";
$pipeliner->add_commands(new Command($cmd, "enhance.ok"));
$cmd = "$utildir/feature_scoring.+-.pl "
. " --features_plus $out_prefix.enhanced.+.features "
. " --features_minus $out_prefix.-.features "
. " --atg_position $pwm_left "
. " > $out_prefix.enhanced.feature.scores";
$pipeliner->add_commands(new Command($cmd, "enhanced_score_features.ok"));
$cmd = "$utildir/feature_scores_to_ROC.pl $out_prefix.enhanced.feature.scores > $out_prefix.enhanced.feature.scores.roc";
$pipeliner->add_commands(new Command($cmd, "enhanced_roc_features.ok"));
$cmd = "$utildir/plot_ROC.Rscript $out_prefix.enhanced.feature.scores.roc || :";
$pipeliner->add_commands(new Command($cmd, "enhanced_rocplot.ok"));
$cmd = "$utildir/compute_AUC.pl $out_prefix.enhanced.feature.scores.roc";
$pipeliner->add_commands(new Command($cmd, "enhanced_aucplot.ok"));
$cmd = "$utildir/make_seqLogo.Rscript $out_prefix.enhanced.+.pwm || :";
$pipeliner->add_commands(new Command($cmd, "seqlogo.enhanced.+.ok"));
$pipeliner->run();
exit(0);
}
|
