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/ /_/ > | \// __ \| | / /_/ | | || |
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/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-135- # convert to tabular input format
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted:136: #`ruby ../ruby/blast_file_parser_concatfiles.rb $outfile_path.blastresults > $outfile_path.tabularresults`;
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-137- {
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-146- print "-> jumpstarting from BLAST results!\n";
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted:147: #`ruby ../ruby/blast_file_parser_concatfiles.rb $jumpstart > $outfile_path.tabularresults`;
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-148- {
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-180-
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted:181:#my $predictor_out = `cd ..; java -jar pp2.jar pp2.prediction.knn.KNNPredictor -i $outfile_path.tabularresults -o $outfile_path.raw $knn -d $distribution -c $closure -t $goterms`;
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-182-
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-236-print `@cmd`; if($?){ confess("@cmd failed: ".($?>>8)); }
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted:237:#print `java -classpath '.' pp2.datahandler.GenerateCAFAOutput -m 1 -i $outfile_path.raw.leaves -o $outfile_path.predicted_allnodes -c $scorecolumn -pr $precision -rc $recall -gc $closure -gn $goterms`;
metastudent-2.0.1/metastudentPkg/lib/groupB/run/knn_weighted-238-
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-4681-4681 Ran GTPase binding molecular_function GO:0008536 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:4682:4682 cytoplasm cellular_component GO:0005737 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-4683-4683 importin cellular_component GO:0005646 1 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-4689-4689 nuclear lamina cellular_component GO:0005652 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:4690:4690 nucleoplasm cellular_component GO:0005654 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-4691-4691 nucleolar ribonuclease P complex cellular_component GO:0005655 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-5961-5961 negative regulation of axonemal microtubule depolymerization biological_process GO:0007027 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:5962:5962 cytoplasm organization biological_process GO:0007028 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-5963-5963 endoplasmic reticulum organization biological_process GO:0007029 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-6225-6225 oocyte anterior/posterior axis specification biological_process GO:0007314 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:6226:6226 pole plasm assembly biological_process GO:0007315 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:6227:6227 pole plasm RNA localization biological_process GO:0007316 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:6228:6228 regulation of pole plasm oskar mRNA localization biological_process GO:0007317 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:6229:6229 pole plasm protein localization biological_process GO:0007318 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-6230-6230 negative regulation of oskar mRNA translation biological_process GO:0007319 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-11006-11006 brain-specific angiogenesis inhibitor activity molecular_function GO:0016527 1 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:11007:11007 sarcoplasm cellular_component GO:0016528 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-11008-11008 sarcoplasmic reticulum cellular_component GO:0016529 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-12602-12602 mitochondrial RNA localization biological_process GO:0019093 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:12603:12603 pole plasm mRNA localization biological_process GO:0019094 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:12604:12604 pole plasm mitochondrial rRNA localization biological_process GO:0019095 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:12605:12605 pole plasm mitochondrial lrRNA localization biological_process GO:0019096 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:12606:12606 pole plasm mitochondrial srRNA localization biological_process GO:0019097 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-12607-12607 reproductive behavior biological_process GO:0019098 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-14556-14556 kynureninase activity molecular_function GO:0030429 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:14557:14557 host cell cytoplasm cellular_component GO:0030430 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-14558-14558 sleep biological_process GO:0030431 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-16078-16078 cortical protein anchoring biological_process GO:0032065 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:16079:16079 nucleolus to nucleoplasm transport biological_process GO:0032066 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-16080-16080 Type IV site-specific deoxyribonuclease activity molecular_function GO:0032067 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-16834-16834 distributive segregation biological_process GO:0032837 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:16835:16835 cell projection cytoplasm cellular_component GO:0032838 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:16836:16836 dendrite cytoplasm cellular_component GO:0032839 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-16837-16837 intramolecular proline-rich ligand binding molecular_function GO:0032840 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-17647-17647 host cell chloroplast thylakoid membrane cellular_component GO:0033654 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:17648:17648 host cell cytoplasm part cellular_component GO:0033655 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-17649-17649 modification by symbiont of host chloroplast biological_process GO:0033656 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-20189-20189 taxoid 7beta-hydroxylase activity molecular_function GO:0036239 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:20190:20190 septal periplasm cellular_component GO:0036240 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-20191-20191 glutamate catabolic process to 4-hydroxybutyrate biological_process GO:0036241 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-20828-20828 nuclear viral factory cellular_component GO:0039715 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:20829:20829 viroplasm viral factory cellular_component GO:0039716 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-20830-20830 spherule viral factory cellular_component GO:0039717 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22021-22021 extracellular non-membrane-bounded organelle cellular_component GO:0043264 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:22022:22022 ectoplasm cellular_component GO:0043265 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22023-22023 regulation of potassium ion transport biological_process GO:0043266 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22761-22761 interaction with host via substance released by membrane budding biological_process GO:0044052 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:22762:22762 translocation of peptides or proteins into host cell cytoplasm biological_process GO:0044053 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22763-22763 rounding by symbiont of host cells biological_process GO:0044054 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22802-22802 host cell nuclear part cellular_component GO:0044094 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:22803:22803 host cell nucleoplasm cellular_component GO:0044095 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22804-22804 type IV pilus cellular_component GO:0044096 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22807-22807 polar tube cellular_component GO:0044099 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:22808:22808 sporoplasm cellular_component GO:0044100 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22809-22809 (R)-citramalyl-CoA lyase activity molecular_function GO:0044101 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22919-22919 host cell plasmodesma cellular_component GO:0044219 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:22920:22920 host cell perinuclear region of cytoplasm cellular_component GO:0044220 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-22921-22921 host cell synapse cellular_component GO:0044221 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-23138-23138 microtubule organizing center part cellular_component GO:0044450 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:23139:23139 nucleoplasm part cellular_component GO:0044451 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-23140-23140 nucleolar part cellular_component GO:0044452 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-23917-23917 bicoid mRNA localization biological_process GO:0045450 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:23918:23918 pole plasm oskar mRNA localization biological_process GO:0045451 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-23919-23919 bone resorption biological_process GO:0045453 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-23961-23961 photoreceptor cell maintenance biological_process GO:0045494 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:23962:23962 pole plasm cellular_component GO:0045495 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-23963-23963 male analia development biological_process GO:0045496 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-24299-24299 positive regulation of bicoid mRNA localization biological_process GO:0045854 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:24300:24300 negative regulation of pole plasm oskar mRNA localization biological_process GO:0045855 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:24301:24301 positive regulation of pole plasm oskar mRNA localization biological_process GO:0045856 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-24302-24302 negative regulation of molecular function, epigenetic biological_process GO:0045857 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-25019-25019 mandelonitrile lyase activity molecular_function GO:0046593 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:25020:25020 maintenance of pole plasm mRNA location biological_process GO:0046594 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:25021:25021 establishment of pole plasm mRNA localization biological_process GO:0046595 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-25022-25022 regulation of viral entry into host cell biological_process GO:0046596 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-26698-26698 cell maturation biological_process GO:0048469 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:26699:26699 perinuclear region of cytoplasm cellular_component GO:0048471 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-26700-26700 threonine-phosphate decarboxylase activity molecular_function GO:0048472 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-30325-30325 long term synaptic depression biological_process GO:0060292 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:30326:30326 germ plasm cellular_component GO:0060293 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-30327-30327 cilium movement involved in cell motility biological_process GO:0060294 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-33893-33893 chaperone-mediated protein transport across periplasmic space biological_process GO:0072323 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:33894:33894 ascus epiplasm cellular_component GO:0072324 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-33895-33895 vulval cell fate commitment biological_process GO:0072325 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-34655-34655 entry of viral genome into host nucleus via docking of viral capsid to the nuclear pore complex and injection of viral genome biological_process GO:0075507 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:34656:34656 entry of viral genome into host nucleus via retainment of capsid in nuclear pore complex and release of genome into nucleoplasm biological_process GO:0075508 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-34657-34657 endocytosis involved in viral entry into host cell biological_process GO:0075509 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-35575-35575 phagocytic vesicle lumen cellular_component GO:0097013 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:35576:35576 ciliary cytoplasm cellular_component GO:0097014 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:35577:35577 bacterial-type flagellar cytoplasm cellular_component GO:0097015 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-35578-35578 L27 domain binding molecular_function GO:0097016 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-36185-36185 maintenance of protein complex location biological_process GO:0098544 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:36186:36186 maintenance of protein complex location in cytoplasm biological_process GO:0098545 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-36187-36187 2',5-3',5'-cyclic GMP-AMP binding molecular_function GO:0098546 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-38540-38540 DNA ligation involved in nuclear cell cycle DNA replication biological_process GO:1902333 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:38541:38541 fructose export from vacuole to cytoplasm biological_process GO:1902334 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-38542-38542 positive chemotaxis involved in neuron migration biological_process GO:1902335 1 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-39033-39033 G-protein coupled receptor catabolic process biological_process GO:1990172 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt:39034:39034 protein localization to nucleoplasm biological_process GO:1990173 0 0 0
metastudent-2.0.1/metastudentPkg/lib/groupB/data/goterm2014.txt-39035-39035 phosphodiesterase decapping endonuclease activity molecular_function GO:1990174 0 0 0
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper2.pl-20-my @cmd = qq|exercise3.pl $targets $filename -e0.1 -h0.1 -j2 $database|;
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper2.pl:21:system(@cmd) && confess("@cmd failed: ".($?>>8));
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper2.pl-22-
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupC/validate.pl-76-my @cmd = qq|/mnt/opt/data/pp2_exercise/groups/groupC/CafaWrapper3.pl $train $outfile $outfolder|;
metastudent-2.0.1/metastudentPkg/lib/groupC/validate.pl:77:system(@cmd) && confess("@cmd failed: ".($?>>8));
metastudent-2.0.1/metastudentPkg/lib/groupC/validate.pl-78-#unlink($outfile);
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper3_new.pl-11-my @cmd = qq|exercise3.pl $database $tmpDir/blast.out|;
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper3_new.pl:12:system(@cmd) && confess("@cmd failed: ".($?>>8));
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper3_new.pl-13-
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper1.pl-20-my @cmd = qq|exercise3.pl $targets $filename -e0.1 -h0.1 -j2 $database|;
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper1.pl:21:system(@cmd) && confess("@cmd failed: ".($?>>8));
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper1.pl-22-
##############################################
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper3.pl-11-my @cmd = qq|./exercise3.pl $database $tmpDir/blast.out|;
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper3.pl:12:system(@cmd) && confess("@cmd failed: ".($?>>8));
metastudent-2.0.1/metastudentPkg/lib/groupC/CafaWrapper3.pl-13-
##############################################
metastudent-2.0.1/debian/tests/run-unit-test-18-for lnk in `find . -type l -name "*.gz"` ; do
metastudent-2.0.1/debian/tests/run-unit-test:19: ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'`
metastudent-2.0.1/debian/tests/run-unit-test-20- rm $lnk