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#! /usr/bin/perl
use Apache::Bio::Tools::PSort ();
use Apache::RPC::Server ();
use Apache::Registry ();
use Apache::Constants ();
use Apache ();
use strict;
my $PSORT_ROOT = "/usr/lib/psort";
my $BLAST_DIR = "/usr/bin";
my $PFTOOLS_DIR = "/usr/bin";
our %ENV;
MAIN: {
my $hmmfile = "$PSORT_ROOT/conf/analysis/modhmm/S_TMHMM_0.92b.hmg";
my $repfile = "$PSORT_ROOT/conf/analysis/modhmm/replacement_letter_multi.rpl";
my $hmmpath = "$PSORT_ROOT/conf/analysis/modhmm/";
my $motifdbp = "$PSORT_ROOT/conf/analysis/motif/grampos/motifs.txt";
my $motifdbn = "$PSORT_ROOT/conf/analysis/motif/gramneg/motifs.txt";
my $sighmmp = "$PSORT_ROOT/conf/analysis/signal/grampos/model.hmm";
my $sigsvmp = "$PSORT_ROOT/conf/analysis/signal/grampos/model.svm";
my $sighmmn = "$PSORT_ROOT/conf/analysis/signal/gramneg/model.hmm";
my $sigsvmn = "$PSORT_ROOT/conf/analysis/signal/gramneg/model.svm";
my $sigprogp = "$PSORT_ROOT/conf/analysis/signal/grampos/check-sig";
my $sigprogn = "$PSORT_ROOT/conf/analysis/signal/gramneg/check-sig";
my $scldbp = "$PSORT_ROOT/conf/analysis/sclblast/grampos/sclblast";
my $scldbn = "$PSORT_ROOT/conf/analysis/sclblast/gramneg/sclblast";
my $ompdb = "$PSORT_ROOT/conf/analysis/omp-motif/omp-motifs.txt";
my $pfscan = "$PFTOOLS_DIR/pfscan";
my $profiledbp = "$PSORT_ROOT/conf/analysis/profile/grampos/ps_ALL";
my $profileidsp = "$PSORT_ROOT/conf/analysis/profile/grampos/profile_ids";
my $profiledbn = "$PSORT_ROOT/conf/analysis/profile/gramneg/ps_ALL";
my $profileidsn = "$PSORT_ROOT/conf/analysis/profile/gramneg/profile_ids";
my $slmodelCn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Cytoplasmic/SVM_MODEL.txt";
my $slpatternsCn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Cytoplasmic/fre_patterns.txt";
my $slmodelIn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Innermembrane/SVM_MODEL.txt";
my $slpatternsIn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Innermembrane/fre_patterns.txt";
my $slmodelOn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Outermembrane/SVM_MODEL.txt";
my $slpatternsOn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Outermembrane/fre_patterns.txt";
my $slmodelEn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Extracellular/SVM_MODEL.txt";
my $slpatternsEn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Extracellular/fre_patterns.txt";
my $slmodelPn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Periplasmic/SVM_MODEL.txt";
my $slpatternsPn = "$PSORT_ROOT/conf/analysis/subloc/gramneg/Periplasmic/fre_patterns.txt";
my $slmodelCp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Cytoplasmic/SVM_MODEL.txt";
my $slpatternsCp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Cytoplasmic/fre_patterns.txt";
my $slmodelMp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Membrane/SVM_MODEL.txt";
my $slpatternsMp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Membrane/fre_patterns.txt";
my $slmodelWp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Cellwall/SVM_MODEL.txt";
my $slpatternsWp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Cellwall/fre_patterns.txt";
my $slmodelEp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Extracellular/SVM_MODEL.txt";
my $slpatternsEp = "$PSORT_ROOT/conf/analysis/subloc/grampos/Extracellular/fre_patterns.txt";
my $bayesp = "$PSORT_ROOT/conf/output/bayesian/grampos/bayes.model";
my $bayesn = "$PSORT_ROOT/conf/output/bayesian/gramneg/bayes.model";
$ENV{BLASTDIR} = $BLAST_DIR;
$ENV{PSORT_PFTOOLS} = $PFTOOLS_DIR;
my $psort = Apache::Bio::Tools::PSort->instance();
# Load the various modules. (Note that the second parameter is the modules
# "aliased" name (to allow more than one instance of a given module,
# possibly with different params, in a pathway) and **MUST** agree with the
# names in the Bayes model file. **IF THEY DON'T AGREE YOUR RESULTS WILL
# BE BUNG!**
# Comparison function for SCL-BLASTe
my $SCLSub = sub {
my $res = shift;
if($res->localization =~ /Unknown/) {
return 1;
}
return 0;
};
# Gram negative
$psort->install('SCLBlast', 'SCL-BLAST-', { -database => $scldbn });
$psort->install('SCLBlast', 'SCL-BLASTe-', { -database => $scldbn,
-exact => 1 });
$psort->install('ModHMM', 'ModHMM-', { -hmmfile => $hmmfile,
-repfile => $repfile,
-path => $hmmpath,
-loc => 'CytoplasmicMembrane' });
$psort->install('OMPMotif', 'OMPMotif-', { -database => $ompdb });
$psort->install('Motif', 'Motif-', { -database => $motifdbn });
$psort->install('Profile', 'Profile-', {-database => $profiledbn,
-program => $pfscan,
-profileids => $profileidsn } );
$psort->install('SVMLoc', 'CytoSVM-', { -model => $slmodelCn,
-patterns => $slpatternsCn});
$psort->install('SVMLoc', 'ECSVM-', { -model => $slmodelEn,
-patterns => $slpatternsEn});
$psort->install('SVMLoc', 'CMSVM-', { -model => $slmodelIn,
-patterns => $slpatternsIn});
$psort->install('SVMLoc', 'OMSVM-', { -model => $slmodelOn,
-patterns => $slpatternsOn});
$psort->install('SVMLoc', 'PPSVM-', { -model => $slmodelPn,
-patterns => $slpatternsPn});
$psort->install('Signal', 'Signal-', { -svm => $sigsvmn, -hmm => $sighmmn,
-program => $sigprogn });
$psort->add_path("psortn", "analysis", ['SCL-BLASTe-', $SCLSub,
['SCL-BLAST-', sub { 1 },
['ModHMM-', sub { 1 },
['OMPMotif-', sub { 1 },
['Motif-', sub { 1 },
['Profile-', sub { 1 },
['CytoSVM-', sub { 1 } ,
['CMSVM-', sub { 1 } ,
['PPSVM-', sub { 1 } ,
['OMSVM-', sub { 1 } ,
['ECSVM-', sub { 1 } ,
['Signal-']]]]]]]]]]]]);
$psort->install('Bayesian', 'Bayesian-', {-model => $bayesn });
$psort->add_path("bayesn", "output", ['Bayesian-', sub { 1 }]);
# Gram positive
$psort->install('ModHMM', 'ModHMM+', { -hmmfile => $hmmfile,
-repfile => $repfile,
-path => $hmmpath,
-loc => 'CytoplasmicMembrane' });
$psort->install('SCLBlast', 'SCL-BLAST+', { -database => $scldbp });
$psort->install('SCLBlast', 'SCL-BLASTe+', { -database => $scldbp,
-exact => 1 });
$psort->install('Motif', 'Motif+', { -database => $motifdbp });
$psort->install('Profile', 'Profile+', {-database => $profiledbp,
-program => $pfscan,
-profileids => $profileidsp } );
$psort->install('SVMLoc', 'CytoSVM+', { -model => $slmodelCp,
-patterns => $slpatternsCp});
$psort->install('SVMLoc', 'ECSVM+', { -model => $slmodelEp,
-patterns => $slpatternsEp});
$psort->install('SVMLoc', 'CMSVM+', { -model => $slmodelMp,
-patterns => $slpatternsMp});
$psort->install('SVMLoc', 'CWSVM+', { -model => $slmodelWp,
-patterns => $slpatternsWp});
$psort->install('Signal', 'Signal+', { -svm => $sigsvmp, -hmm => $sighmmp,
-program => $sigprogp, -gram => 'Positive' });
$psort->add_path("psortp", "analysis", ['SCL-BLASTe+', $SCLSub,
['ModHMM+', sub { 1 },
['SCL-BLAST+', sub { 1 },
['Motif+', sub { 1 },
['Profile+', sub { 1 },
['CytoSVM+', sub { 1 } ,
['CMSVM+', sub {1} ,
['ECSVM+', sub {1},
['CWSVM+', sub {1},
['Signal+']
]]]]]]]]]);
$psort->install('Bayesian', 'Bayesian+', {-model => $bayesp });
$psort->add_path("bayesp", "output", ['Bayesian+', sub { 1 }]);
return 1;
}
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