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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh-4-SCRIPT_PATH=$0
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh:5:SCRIPT_PATH=`dirname $SCRIPT_PATH`
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh-6-JAVA_PATH=$SCRIPT_PATH:.
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iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh-10-   MUMMER=`which nucmer`
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh:11:   MUMMER=`dirname $MUMMER`
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh-12-fi
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iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh-24-JAVADIR=/fs/wrenhomes/sergek/Utils
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh:25:GENOMESIZE=`java -cp $JAVA_PATH SizeFasta $REF |awk '{SUM+=$NF; print SUM}'|tail -n 1`
iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh-26-
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iva-1.0.9+ds/iva/ratt/main.ratt.pl-1055-  if (! -d "$path") {
iva-1.0.9+ds/iva/ratt/main.ratt.pl:1056:	!system("mkdir $path") or warn "Couldn't create directory $path.\n";
iva-1.0.9+ds/iva/ratt/main.ratt.pl-1057-  }
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iva-1.0.9+ds/iva/ratt/start.ratt.sh-130-	mkdir tmp
iva-1.0.9+ds/iva/ratt/start.ratt.sh:131:	for x in `grep '>' ../$root.$iteration | sed 's/>//g' | awk '{ print $1 }'` ; do
iva-1.0.9+ds/iva/ratt/start.ratt.sh-132-		cat ../$root.*.$x.gff > ../All.$x.gff;
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iva-1.0.9+ds/iva/ratt/start.ratt.sh-155-NUCMER_EXE=${NUCMER_EXE-`which nucmer 2>/dev/null`}
iva-1.0.9+ds/iva/ratt/start.ratt.sh:156:EMBL_files=${EMBL_files-`ls $refembl/ | wc 2>/dev/null`}
iva-1.0.9+ds/iva/ratt/start.ratt.sh-157-#PERL_SCRIPT=${NUCMER_EXE-`which samtools 2>/dev/null`}
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iva-1.0.9+ds/iva/ratt/start.ratt.sh-435-
iva-1.0.9+ds/iva/ratt/start.ratt.sh:436:for nameRes in `grep '>' $query | perl -nle 's/\|/_/g;/>(\S+)/; print $1'` ; do
iva-1.0.9+ds/iva/ratt/start.ratt.sh-437-	echo "work on $nameRes"
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iva-1.0.9+ds/iva/tests/data/qc_external_test_run_ratt.embl/hiv-1.embl-343-FT                   prevents splicing of viral RNA; shuttles unspliced viral
iva-1.0.9+ds/iva/tests/data/qc_external_test_run_ratt.embl/hiv-1.embl:344:FT                   RNA to the cytoplasm for expression of viral proteins and
iva-1.0.9+ds/iva/tests/data/qc_external_test_run_ratt.embl/hiv-1.embl-345-FT                   incorporation of full length viral genomic RNA into
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iva-1.0.9+ds/iva/tests/graph_test.py-27-    def setUp(self):
iva-1.0.9+ds/iva/tests/graph_test.py:28:        self.asm = assembly.Assembly(contigs_file=os.path.join(data_dir, 'graph_test.contigs.fa'))
iva-1.0.9+ds/iva/tests/graph_test.py-29-        self.g = graph.Graph(self.asm)