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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
trace2dbest-3.0.1/rename_file.pl-108- $new_file.=$file;
trace2dbest-3.0.1/rename_file.pl:109: system("mv $file $new_file");
trace2dbest-3.0.1/rename_file.pl-110- }
##############################################
trace2dbest-3.0.1/rename_file.pl-119- $new_file.=$end;
trace2dbest-3.0.1/rename_file.pl:120: system("mv $file $new_file");
trace2dbest-3.0.1/rename_file.pl-121- }
##############################################
trace2dbest-3.0.1/rename_file.pl-131- $new_file=~s/$txt/$sub/g;
trace2dbest-3.0.1/rename_file.pl:132: system ("mv $file $new_file");
trace2dbest-3.0.1/rename_file.pl-133- }
##############################################
trace2dbest-3.0.1/rename_file.pl-164- $new_file=~s/;/0/g;
trace2dbest-3.0.1/rename_file.pl:165: system ("mv $file $new_file");
trace2dbest-3.0.1/rename_file.pl-166- }
##############################################
trace2dbest-3.0.1/trace2dbest.pl-409- print colored("ERROR: $Lib_file not writeable - trying to fix it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:410: my $lucky = system ("chmod $Lib_file 755");
trace2dbest-3.0.1/trace2dbest.pl-411- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-417- print colored("ERROR: $Lib_file does not exist - trying to create it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:418: my $lucky = system ("touch $Lib_file");
trace2dbest-3.0.1/trace2dbest.pl-419- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-429- print colored("ERROR: $Pub_file not writeable - trying to fix it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:430: my $lucky = system ("chmod $Pub_file 755");
trace2dbest-3.0.1/trace2dbest.pl-431- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-437- print colored("ERROR: $Pub_file does not exist - trying to create it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:438: my $lucky = system ("touch $Pub_file");
trace2dbest-3.0.1/trace2dbest.pl-439- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-449- print colored("ERROR: $Cont_file not writeable - trying to fix it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:450: my $lucky = system ("chmod $Cont_file 755");
trace2dbest-3.0.1/trace2dbest.pl-451- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-457- print colored("ERROR: $Cont_file does not exist - trying to create it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:458: my $lucky = system ("touch $Cont_file");
trace2dbest-3.0.1/trace2dbest.pl-459- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-469- print colored("ERROR: $EST_file not writeable - trying to fix it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:470: my $lucky = system ("chmod $EST_file 755");
trace2dbest-3.0.1/trace2dbest.pl-471- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-477- print colored("ERROR: $EST_file does not exist - trying to create it\n","red bold");
trace2dbest-3.0.1/trace2dbest.pl:478: my $lucky = system ("touch $EST_file");
trace2dbest-3.0.1/trace2dbest.pl-479- unless ($lucky) {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-929-#see below (sequence processing) for explaination of phred arguements
trace2dbest-3.0.1/trace2dbest.pl:930: system("phred -id $tracedir $phredoptions "); #exit_nomatch means phred will exit if the trace chemistry is not found in phredpar.dat
trace2dbest-3.0.1/trace2dbest.pl-931-
##############################################
trace2dbest-3.0.1/trace2dbest.pl-959- print "Running cross_match (screening for vector sequence) - please wait...";
trace2dbest-3.0.1/trace2dbest.pl:960: system("cross_match all.seq $vector_file -minmatch $vminmatch -minscore $vminscore -screen 2>>cmlogfile 1> /dev/null");
trace2dbest-3.0.1/trace2dbest.pl-961- if (-s "all.seq.screen") {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-989- print "Running cross_match (screening for E. coli sequence) - please wait...";
trace2dbest-3.0.1/trace2dbest.pl:990: system("cross_match all.n $ecoli_file -minmatch $eminmatch -minscore $eminscore -screen 2>>cmlogfile 1> /dev/null");
trace2dbest-3.0.1/trace2dbest.pl-991- if (-s "all.n.screen") {
##############################################
trace2dbest-3.0.1/trace2dbest.pl-2074-
trace2dbest-3.0.1/trace2dbest.pl:2075: unless (-e "$db_file") {system ("touch $db_file")}
trace2dbest-3.0.1/trace2dbest.pl-2076- open (DBFILE, "$db_file") or die "Error: $db_file could not be opened!\n";
##############################################
trace2dbest-3.0.1/trace2dbest.pl-2965- print "Local BLAST of $file ...\n";
trace2dbest-3.0.1/trace2dbest.pl:2966: system("blastall -p blastx -d $blast_db -i temp.seq -o blast.out -T F");
trace2dbest-3.0.1/trace2dbest.pl-2967- }
##############################################
trace2dbest-3.0.1/trace2dbest.pl-3119-
trace2dbest-3.0.1/trace2dbest.pl:3120: system ("mv raw_traces $location/raw_traces");
trace2dbest-3.0.1/trace2dbest.pl-3121-
##############################################
trace2dbest-3.0.1/trace2dbest.pl-3134-
trace2dbest-3.0.1/trace2dbest.pl:3135:#system("less $basedir/trace2dbest_UG.txt");
trace2dbest-3.0.1/trace2dbest.pl-3136-#temporarily disabled - incompatibility with some unix tastes