===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-139- $tmp=~s/\/$//g;
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:140: system("setenv BLASTDB $tmp");}
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-141- # ------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-463- ($Lok,$msgSys)=
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:464: &sysSystem("$command" ,$fhTraceLoc);
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-465- if (! $Lok){
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-480- $msg=
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:481: system("$command");
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-482-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-492- $size=$tmp[8];
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:493: $first_line=system("head -1 $fileOutFilLoc");
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-494- return(2,"none found")
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-612- $tmp=~s/\/$//g;
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:613: system("setenv BLASTDB $tmp");}
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-614- # ------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-740- # set env
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:741:# system("setenv BLASTMAT $BLASTMATloc"); # system call
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-742- $ENV{'BLASTMAT'}=$BLASTMATloc;
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-743-
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:744:# system("setenv BLASTDB $BLASTDBloc"); # system call
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-745- $ENV{'BLASTDB'}=$BLASTDBloc;
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-1864- unlink ($file) ; $msgHere.="--- $sbrName: unlink($file)\n";}
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:1865: system("\\rm MAX*$jobid");
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-1866- $msgHere.="--- $sbrName: system '\\rm MAX*$jobid'\n" ;}
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-2195- ($Lok,$msg)=
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:2196: &sysSystem("$cmd",$fhoutSbr);
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-2197-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-2247- print $fhErrSbr "--- $sbrName: system \t $cmd\n";
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl:2248: system("$cmd");
profphd-1.0.42/src/prof/embl/scr/lib/molbio.pl-2249- # ------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-122- $#tmp=$#tmp2=0;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:123: @tmp2=`ls -a1 $dirLoc`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-124- $dirLocTmp=$dirLoc; $dirLocTmp.="/" if ($dirLocTmp !~/\/$/);
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-278-
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:279: foreach $tmp(@tmp){$ls=`ls -l $tmp`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-280- push(@tmp2,"$ls");}
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-362-
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:363: foreach $tmp(@tmp){$ls=`ls -l $tmp`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-364- push(@tmp2,"$ls");}
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-417- # ------------------------------
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:418: $tmp=`grep '^SEQLENGTH' $fileInLoc`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-419- if( $? ){ Carp::confess( "grep '^SEQLENGTH' $fileInLoc failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-455- # ------------------------------
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:456: $tmp=`grep '^NALIGN' $fileInLoc`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-457- if( $? ){ Carp::confess( "grep '^NALIGN' $fileInLoc failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-489- # ------------------------------
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:490: $tmp=`grep '^ .*[0-9]* : .* [0-9][A-Z0-9][A-Z0-9][A-Z0-9] ' $fileInLoc`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-491- if( $? ){ Carp::confess( "grep '^ .*[0-9]* : .* [0-9][A-Z0-9][A-Z0-9][A-Z0-9] ' $fileInLoc failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-537- # ------------------------------
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:538: $tmp=`grep 'RESOLUTION\. ' $fileInLoc`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-539- if( $? ){ Carp::confess( "grep 'RESOLUTION\. ' $fileInLoc failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-631- foreach $fileToCat (@fileToCat){
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:632: $Lok= system("$niceLoc cat < $fileToCat >> $fileToCatTo");
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-633- if( $Lok ){ Carp::confess( "cmd $niceLoc cat < $fileToCat >> $fileToCatTo failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-661- my $_cmd = "$niceLoc \\cp $fileToCopy $fileToCopyTo";
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:662: $Lok= system( $_cmd );
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-663- if( $Lok ){ Carp::confess( "cmd $_cmd failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-705- $Lok=
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:706: require($exe_ctime)
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-707- if (-e $exe_ctime); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-748- # run
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:749: system( $cmd ) && Carp::confess( "cmd $cmd failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-750- return(1,"ok",$prt);
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-825- $Lok= mkdir ($argIn, 0770 );
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:826: system("chmod u+rwx $argIn");
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:827: system("chmod go+rx $argIn");
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-828-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-848-
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:849: system("$niceLoc \\mv $fileToCopy $fileToCopyTo") && Carp::confess( "cmd $niceLoc \\mv $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-850-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-874- sleep 60;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:875: system( $cmd ) && Carp::confess( "cmd $cmd failed: ".( $? >> 8 ) );}
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-876- return(1) if (! -d $dirLoc);
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-954- $message.="*** from sysSendMailAlarm (lib-x.pl)\n"."***$message\n";
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:955: system("echo '$messageLoc' | $exe_mailLoc -s PP_ERROR $userLoc") && Carp::confess( "cmd echo '$messageLoc' | $exe_mailLoc -s PP_ERROR $userLoc failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-956- return(1,"ok $sbrName");
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-965-# sysSystem simple way of running system command + documenting them
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:966:# in: $cmd: will do system($cmd)
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-967-# in: $fhLoc: will write trace onto fhLoc
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-987- $Lsystem=
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:988: system( $cmdLoc ) && Carp::confess( "cmd $cmdLoc failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-989-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-1010- $command="$cmdUntarLoc $fileTarLoc\n"; print "--- $sbrName system \t '$command'\n";
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:1011: @list=`$command`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-1012- if( $? ){ Carp::confess( "$command failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-1052- $command="$cmdTarLoc $fileTarLoc $list\n";print "--- $sbrName system \t '$command'\n";
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl:1053: $Lok=`$command`;
profphd-1.0.42/src/prof/embl/scr/lib/sys.pl-1054- if( $? ){ Carp::confess( "$command failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-1747- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/src/prof/embl/scr/lib/br.pl:1748:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/src/prof/embl/scr/lib/br.pl:1749:# system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-1750- }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-4757-
profphd-1.0.42/src/prof/embl/scr/lib/br.pl:4758: if ($Lscreen) {print "--- wrt_phd2msf \t 'system ($exePhd2Msf $arg)'\n";}
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-4759-
profphd-1.0.42/src/prof/embl/scr/lib/br.pl:4760: system("$exePhd2Msf $arg");
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-4761- return(1," ");
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-4883- $sym{"PHD htm"}="HTM's predicted by the PHD neural network\n".
profphd-1.0.42/src/prof/embl/scr/lib/br.pl:4884: "--- system ($symh=HTM, ' '=not HTM)";
profphd-1.0.42/src/prof/embl/scr/lib/br.pl-4885- $sym{"Rel htm"}="Reliability index of prediction (0-9, 0 is low)";
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-482- if ($exeConv=~/\.pl/){
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl:483: system("$exeConv $fileFssp $dirDsspLoc >> $fileDafTmp"); }
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-484- # ------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-640-# "' | $exeConvLoc";
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl:641:# $fhErrSbr=`$command`;
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-642-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-916- # system call
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl:917: system("$cmd");
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-918-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-962- # system call
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl:963: system("$cmd");
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-964-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-1068-# $command="echo '$fileMsfLoc\n$form_out\n$matGCG\n$an\n$fileHsspLoc\n \n$an\n' | $exeConvLoc";
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl:1069:# $fhErrSbrx=`$command`;
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-1070- # --------------------------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-6267-# print $fhoutSbr "--- $sbrName3: system '$cmd'\n" if ($fhoutSbr);
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl:6268:# system("$cmd");
profphd-1.0.42/src/prof/embl/scr/lib/formats.pl-6269-# }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/hssp.pl-436- $cmd="\\mv $filetmp $fileInLoc";
profphd-1.0.42/src/prof/embl/scr/lib/hssp.pl:437: system($cmd);
profphd-1.0.42/src/prof/embl/scr/lib/hssp.pl-438- print "--- $sbrName: system '$cmd'\n"
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/scr.pl-1485- $scr=$exePvmgetarch;
profphd-1.0.42/src/prof/embl/scr/lib/scr.pl:1486: $archFound=`$scr`; # system call
profphd-1.0.42/src/prof/embl/scr/lib/scr.pl-1487- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/lib/scr.pl-1517- $scr=$exePvmgetarch;
profphd-1.0.42/src/prof/embl/scr/lib/scr.pl:1518: $archFound=`$scr`; # system call
profphd-1.0.42/src/prof/embl/scr/lib/scr.pl-1519- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/phd_htmref.pm-1200- foreach $tmp(@tmp){
profphd-1.0.42/src/prof/embl/scr/pack/phd_htmref.pm:1201: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/src/prof/embl/scr/pack/phd_htmref.pm-1202- last;}}
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/phd_htmtop.pm-1071- print "--- system: '$exe $file_in $arg'\n" if ($Lscreen);
profphd-1.0.42/src/prof/embl/scr/pack/phd_htmtop.pm:1072: system("$exe $file_in $arg");
profphd-1.0.42/src/prof/embl/scr/pack/phd_htmtop.pm-1073- return($file_out) if (-e $file_out);
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-2270- if ($exeConv=~/\.pl/){
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm:2271: system("$exeConv $fileFssp $dirDsspLoc >> $fileDafTmp"); }
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-2272- # ------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-4463- $scr=$exePvmgetarch;
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm:4464: $archFound=`$scr`; # system call
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-4465- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-4495- $scr=$exePvmgetarch;
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm:4496: $archFound=`$scr`; # system call
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-4497- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-4555- ($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm:4556: return(0,"*** ERROR $sbrName: failed to run system ($cmd)\n".$msg."\n")
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-4557- if (! $Lok || ! -e $fileTmpLoc);
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-7207- foreach $tmp(@tmp){
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm:7208: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/src/prof/embl/scr/pack/copf.pm-7209- last;}}
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-1722- $scr=$exePvmgetarch;
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm:1723: $archFound=`$scr`; # system call
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-1724- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-1754- $scr=$exePvmgetarch;
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm:1755: $archFound=`$scr`; # system call
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-1756- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-2597-
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm:2598: $Lok= system("$niceLoc \\cp $fileToCopy $fileToCopyTo");
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-2599-# return(0,"*** $sbrName: fail copy '$fileToCopy -> $fileToCopyTo' ($Lok)!") if (! $Lok);
##############################################
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-2621- foreach $tmp(@tmp){
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm:2622: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/src/prof/embl/scr/pack/hssp_filter.pm-2623- last;}}
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_phd2ascii.pl-32- next if (! -e $dir.$lib);
profphd-1.0.42/src/prof/embl/scr/conv_phd2ascii.pl:33: $Lok=require($dir.$lib); }
profphd-1.0.42/src/prof/embl/scr/conv_phd2ascii.pl-34-die("*** ERROR $scrName: could NOT find lib=$lib!\n") if (! $Lok);
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_phd2ascii.pl-373- $dir=~s/\/$//g;
profphd-1.0.42/src/prof/embl/scr/conv_phd2ascii.pl:374: system("mkdir $dir");}}
profphd-1.0.42/src/prof/embl/scr/conv_phd2ascii.pl-375-
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_phd2casp2.pl-46- if (-e $filePhd2){
profphd-1.0.42/src/prof/embl/scr/conv_phd2casp2.pl:47: $nalignGrep=`grep NALIGN $filePhd2`;
profphd-1.0.42/src/prof/embl/scr/conv_phd2casp2.pl-48- if (defined $nalignGrep && $nalignGrep=~/\d/){
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_phd2casp4.pl-46- if (-e $filePhd2){
profphd-1.0.42/src/prof/embl/scr/conv_phd2casp4.pl:47: $nalignGrep=`grep NALIGN $filePhd2`;
profphd-1.0.42/src/prof/embl/scr/conv_phd2casp4.pl-48- if (defined $nalignGrep && $nalignGrep=~/\d/){
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_phd2html.pl-38- next if (! -e $dir.$lib);
profphd-1.0.42/src/prof/embl/scr/conv_phd2html.pl:39: $Lok=require($dir.$lib); }
profphd-1.0.42/src/prof/embl/scr/conv_phd2html.pl-40-die("*** ERROR $scrName: could NOT find lib=$lib!\n") if (! $Lok);
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_phd2html.pl-257- $dir=~s/\/$//g;
profphd-1.0.42/src/prof/embl/scr/conv_phd2html.pl:258: system("mkdir $dir");}}
profphd-1.0.42/src/prof/embl/scr/conv_phd2html.pl-259-
##############################################
profphd-1.0.42/src/prof/embl/scr/conv_rdb2pred.pl-546- foreach $tmp(@tmp){
profphd-1.0.42/src/prof/embl/scr/conv_rdb2pred.pl:547: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/src/prof/embl/scr/conv_rdb2pred.pl-548- last;}}
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-68- print "crossCpArchis: system 'cp $para_ok_sec $tmp'\n";
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl:69: system("cp $para_ok_sec $tmp") && Carp::confess("cmd cp $para_ok_sec $tmp failed: ".( $? >> 8 ) ); }}
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-70- if ($Lacc) {
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-77- print "crossCpArchis: system 'cp $para_ok_sec $tmp'\n";
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl:78: system("cp $para_ok_acc $tmp") && Carp::confess("cmd cp $para_ok_acc $tmp failed: ".( $? >> 8 ) ); }}
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-79- # ------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-99- print "--- trying to copy:$tmp_file, to local:$tmp \n";
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl:100: system("\\cp $tmp_file* $tmp") && Carp::confess( "cmd \\cp $tmp_file* $tmp failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-101- print "--- trying to unzip: $tmp\n";
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl:102: system("gunzip $tmp") && Carp::confess( "cmd gunzip $tmp failed: ".( $? >> 8) ); }
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-103- push(@file_clean,"$tmp2"); }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-125- print "--- trying to copy:$tmp_file, to local:$tmp \n";
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl:126: system("\\cp $tmp_file* $tmp") && Carp::confess( "\\cp $tmp_file* $tmp failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-127- print "--- trying to unzip: $tmp\n";
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl:128: system("gunzip $tmp") && Carp::confess( "cmd gunzip $tmp failed: ".( $? >> 8) ); }
profphd-1.0.42/src/prof/embl/scr/lib-phd.pl-129- push(@file_clean,"$tmp2"); }
##############################################
profphd-1.0.42/src/prof/embl/scr/test-install.pl-200- $cmd="diff ".$filePhd[$it]." $exa";
profphd-1.0.42/src/prof/embl/scr/test-install.pl:201: @tmp=`$cmd`;
profphd-1.0.42/src/prof/embl/scr/test-install.pl-202- foreach $tmp (@tmp){
##############################################
profphd-1.0.42/src/prof/embl/scr/test-install.pl-211- $cmd="diff ".$fileRdb[$it]." $exa";
profphd-1.0.42/src/prof/embl/scr/test-install.pl:212: @tmp=`$cmd`;
profphd-1.0.42/src/prof/embl/scr/test-install.pl-213- foreach $tmp (@tmp){
##############################################
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl-144- # read hssp
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl:145: $tmp=`grep '^NALIGN ' $hssp`;
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl-146- $tmp=~s/[\s\n]*$//g;
##############################################
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl-185- $cmd="\\mv ".$fileIn." ".$old;
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl:186: system("$cmd"); print "--- system '$cmd'\n" if ($Ldebug);
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl-187- $new=$fileIn;
##############################################
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl-189- $cmd="\\mv ".$fileOut." ".$new;
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl:190: system("$cmd"); print "--- system '$cmd'\n" if ($Ldebug);
profphd-1.0.42/src/prof/embl/scr/tlphd-add-nali2rdb.pl-191-}
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-223-# "' | $exeConvLoc";
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:224:# $fhErrSbr=`$command`;
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-225-
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-266-# $command="echo '$fileMsfLoc\n$form_out\n$matGCG\n$an\n$fileHsspLoc\n \n$an\n' | $exeConvLoc";
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:267:# $fhErrSbrx=`$command`;
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-268- # --------------------------------------------------
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-3495- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:3496:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:3497: system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-3498- }
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5446-
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:5447: $Lok= system( "cp", $fileToCopy, $fileToCopyTo ) && Carp::confess( "cmd cp $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ));
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5448-# return(0,"*** $sbrName: fail copy '$fileToCopy -> $fileToCopyTo' ($Lok)!") if (! $Lok);
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5470- foreach $tmp(@tmp){
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:5471: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5472- last;}}
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5502- return(0,"*** $sbrName: needs 2 arg 'fToCopy fToCopyTo'!") if (! defined $fileToCopyTo);
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:5503: system("$niceLoc \\mv $fileToCopy $fileToCopyTo") && Carp::confess( "cmd $niceLoc \\mv $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ));
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5504- if (! -e $fileToCopyTo){
##############################################
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5717- $sym{"PHD htm"}="HTM's predicted by the PHD neural network\n".
profphd-1.0.42/src/prof/embl/scr/lib-col.pl:5718: "--- system ($symh=HTM, ' '=not HTM)";
profphd-1.0.42/src/prof/embl/scr/lib-col.pl-5719- $sym{"Rel htm"}="Reliability index of prediction (0-9, 0 is low)";
##############################################
profphd-1.0.42/src/prof/embl/phd.pl-140- # yy: make this a real file!!!
profphd-1.0.42/src/prof/embl/phd.pl:141:# system("echo $fileHssp >> files-with-problems.list");
profphd-1.0.42/src/prof/embl/phd.pl-142-
##############################################
profphd-1.0.42/src/prof/embl/phd.pl-228-
profphd-1.0.42/src/prof/embl/phd.pl:229: $Lok= require($par{"$lib"});
profphd-1.0.42/src/prof/embl/phd.pl-230-
##############################################
profphd-1.0.42/src/prof/embl/phd.pl-359- $scr="/home/phd/ut/phd/scr/which_arch.sh" if (! -e $scr);
profphd-1.0.42/src/prof/embl/phd.pl:360: if (-e $scr && -x $scr){ $ARCH=`$scr`;
profphd-1.0.42/src/prof/embl/phd.pl-361- $ARCH=~s/\s|\n//g; }}
##############################################
profphd-1.0.42/src/prof/scr/lib/prof.pm-165- # set general parameters
profphd-1.0.42/src/prof/scr/lib/prof.pm:166: $Lok=require($par{"confProf"});
profphd-1.0.42/src/prof/scr/lib/prof.pm-167-
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-635-# $par{"dirOut"},"'\n" if (! $Lok);
profphd-1.0.42/src/prof/scr/lib/lib-col.pl:636: system( @cmd ) && Carp::confess( "@cmd failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-637- print "--- $sbrName system '@cmd'\n" if ($par{"verb2"});
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-667- my @cmd = ( "mkdir", '-p', '-m', '0755', $tmp );
profphd-1.0.42/src/prof/scr/lib/lib-col.pl:668: system( @cmd ) && Carp::confess( "@cmd failed: ".( $? >> 8 ) );
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-669- print "--- $sbrName system '@cmd'\n" if ($par{"verb2"});
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-3333-
profphd-1.0.42/src/prof/scr/lib/lib-col.pl:3334: $Lok= system("\\cp $fileToCopy $fileToCopyTo");
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-3335- if( $Lok ){ Carp::confess( "cmd \\cp $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-3375- $Lok=
profphd-1.0.42/src/prof/scr/lib/lib-col.pl:3376: require($exe_ctime)
profphd-1.0.42/src/prof/scr/lib/lib-col.pl-3377- if (-e $exe_ctime); }
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl-530- if (length($errMsg)>1){
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl:531: system ("echo '$fileInLoc' >> ".$par{"fileOutErrorBlast"});
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl-532- $msg="*** ERROR $SBR3: FATAL problem BLAST input mat=".
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl-9551- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl:9552:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl:9553: system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl-9554- }
##############################################
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl-10380-# prot2nn_seqLocSalt sums over salt bridges to [ED]-[KL]=1, [KL]-[ED]=1
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl:10381:# i,(i+n) where n=1..$winLoc
profphd-1.0.42/src/prof/scr/lib/lib-prof.pl-10382-# NOTE: =1 if either i-n OR i+n opposite charge
##############################################
profphd-1.0.42/src/prof/scr/pack/tlprof_htmref.pm-1267- foreach $tmp(@tmp){
profphd-1.0.42/src/prof/scr/pack/tlprof_htmref.pm:1268: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/src/prof/scr/pack/tlprof_htmref.pm-1269- last;}}
##############################################
profphd-1.0.42/src/prof/scr/pack/tlprof_htmtop.pm-1143- print "--- system: '$exe $file_in $arg'\n" if ($Lscreen);
profphd-1.0.42/src/prof/scr/pack/tlprof_htmtop.pm:1144: system("$exe $file_in $arg");
profphd-1.0.42/src/prof/scr/pack/tlprof_htmtop.pm-1145- return($file_out) if (-e $file_out);
##############################################
profphd-1.0.42/src/prof/scr/conv_prof.pl-47- next if (! -e $dir.$lib);
profphd-1.0.42/src/prof/scr/conv_prof.pl:48: $Lok=require($dir.$lib);
profphd-1.0.42/src/prof/scr/conv_prof.pl-49- if ($Lok) {
##############################################
profphd-1.0.42/src/prof/scr/conv_prof.pl-168- print "-*- WARN $scrName: move existing output file $fileOut->$fileOutTmp\n";
profphd-1.0.42/src/prof/scr/conv_prof.pl:169: system("\\mv $fileOut $fileOutTmp");
profphd-1.0.42/src/prof/scr/conv_prof.pl-170- }
##############################################
profphd-1.0.42/src/prof/scr/conv_prof.pl-213- print "-*- WARN $scrName: move existing output file $fileOut->$fileOutTmp\n";
profphd-1.0.42/src/prof/scr/conv_prof.pl:214: system("\\mv $fileOut $fileOutTmp");
profphd-1.0.42/src/prof/scr/conv_prof.pl-215- }
##############################################
profphd-1.0.42/src/prof/scr/conv_prof.pl-730- $dir=~s/\/$//g;
profphd-1.0.42/src/prof/scr/conv_prof.pl:731: system("mkdir $dir");}}
profphd-1.0.42/src/prof/scr/conv_prof.pl-732-
##############################################
profphd-1.0.42/src/prof/scr/prof.pl-159- # use package
profphd-1.0.42/src/prof/scr/prof.pl:160:$Lok=require($par{"packProf"});
profphd-1.0.42/src/prof/scr/prof.pl-161-if (! $Lok){
##############################################
profphd-1.0.42/src/prof/scr/test-install.pl-212- $cmd="diff ".$fileProf[$it]." $exa";
profphd-1.0.42/src/prof/scr/test-install.pl:213: @tmp=`$cmd`;
profphd-1.0.42/src/prof/scr/test-install.pl-214- foreach $tmp (@tmp){
##############################################
profphd-1.0.42/src/prof/scr/test-install.pl-223- $cmd="diff ".$fileRdb[$it]." $exa";
profphd-1.0.42/src/prof/scr/test-install.pl:224: @tmp=`$cmd`;
profphd-1.0.42/src/prof/scr/test-install.pl-225- foreach $tmp (@tmp){
##############################################
profphd-1.0.42/src/prof/scr/tlprof_jury.pl-32- next if (! -e $dir.$lib);
profphd-1.0.42/src/prof/scr/tlprof_jury.pl:33: $Lok=require($dir.$lib);
profphd-1.0.42/src/prof/scr/tlprof_jury.pl-34- last if ($Lok);}
##############################################
profphd-1.0.42/src/prof/scr/tlprof_jury.pl-378- $dir=~s/\/$//g;
profphd-1.0.42/src/prof/scr/tlprof_jury.pl:379: system("mkdir $dir");}}
profphd-1.0.42/src/prof/scr/tlprof_jury.pl-380-
##############################################
profphd-1.0.42/src/prof/prof.pl-162- # use package
profphd-1.0.42/src/prof/prof.pl:163:$Lok=require($par{"packProf"});
profphd-1.0.42/src/prof/prof.pl-164-if (! $Lok){
##############################################
profphd-1.0.42/src/prof/profconv-47- next if (! -e $dir.$lib);
profphd-1.0.42/src/prof/profconv:48: $Lok=require($dir.$lib);
profphd-1.0.42/src/prof/profconv-49- if ($Lok) {
##############################################
profphd-1.0.42/src/prof/profconv-168- print "-*- WARN $scrName: move existing output file $fileOut->$fileOutTmp\n";
profphd-1.0.42/src/prof/profconv:169: system("\\mv $fileOut $fileOutTmp");
profphd-1.0.42/src/prof/profconv-170- }
##############################################
profphd-1.0.42/src/prof/profconv-213- print "-*- WARN $scrName: move existing output file $fileOut->$fileOutTmp\n";
profphd-1.0.42/src/prof/profconv:214: system("\\mv $fileOut $fileOutTmp");
profphd-1.0.42/src/prof/profconv-215- }
##############################################
profphd-1.0.42/src/prof/profconv-732- $dir=~s/\/$//g;
profphd-1.0.42/src/prof/profconv:733: system("mkdir $dir");}}
profphd-1.0.42/src/prof/profconv-734-
##############################################
profphd-1.0.42/debian/tests/installation-test-18-for lnk in `find . -type l -name "*.gz"` ; do
profphd-1.0.42/debian/tests/installation-test:19: ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'`
profphd-1.0.42/debian/tests/installation-test-20- rm $lnk
##############################################
profphd-1.0.42/debian/tests/profphd-install-test-22-for lnk in `find . -type l -name "*.gz"` ; do
profphd-1.0.42/debian/tests/profphd-install-test:23: ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'`
profphd-1.0.42/debian/tests/profphd-install-test-24- rm $lnk
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-223-# "' | $exeConvLoc";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:224:# $fhErrSbr=`$command`;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-225-
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-266-# $command="echo '$fileMsfLoc\n$form_out\n$matGCG\n$an\n$fileHsspLoc\n \n$an\n' | $exeConvLoc";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:267:# $fhErrSbrx=`$command`;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-268- # --------------------------------------------------
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-3495- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:3496:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:3497: system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-3498- }
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5446-
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:5447: $Lok= system( "cp", $fileToCopy, $fileToCopyTo ) && Carp::confess( "cmd cp $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ));
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5448-# return(0,"*** $sbrName: fail copy '$fileToCopy -> $fileToCopyTo' ($Lok)!") if (! $Lok);
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5470- foreach $tmp(@tmp){
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:5471: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5472- last;}}
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5502- return(0,"*** $sbrName: needs 2 arg 'fToCopy fToCopyTo'!") if (! defined $fileToCopyTo);
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:5503: system("$niceLoc \\mv $fileToCopy $fileToCopyTo") && Carp::confess( "cmd $niceLoc \\mv $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ));
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5504- if (! -e $fileToCopyTo){
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5717- $sym{"PHD htm"}="HTM's predicted by the PHD neural network\n".
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl:5718: "--- system ($symh=HTM, ' '=not HTM)";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib-col.pl-5719- $sym{"Rel htm"}="Reliability index of prediction (0-9, 0 is low)";
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-1747- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl:1748:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl:1749:# system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-1750- }
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-4757-
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl:4758: if ($Lscreen) {print "--- wrt_phd2msf \t 'system ($exePhd2Msf $arg)'\n";}
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-4759-
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl:4760: system("$exePhd2Msf $arg");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-4761- return(1," ");
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-4883- $sym{"PHD htm"}="HTM's predicted by the PHD neural network\n".
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl:4884: "--- system ($symh=HTM, ' '=not HTM)";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/br.pl-4885- $sym{"Rel htm"}="Reliability index of prediction (0-9, 0 is low)";
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-482- if ($exeConv=~/\.pl/){
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl:483: system("$exeConv $fileFssp $dirDsspLoc >> $fileDafTmp"); }
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-484- # ------------------------------
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-640-# "' | $exeConvLoc";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl:641:# $fhErrSbr=`$command`;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-642-
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-916- # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl:917: system("$cmd");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-918-
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-962- # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl:963: system("$cmd");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-964-
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-1068-# $command="echo '$fileMsfLoc\n$form_out\n$matGCG\n$an\n$fileHsspLoc\n \n$an\n' | $exeConvLoc";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl:1069:# $fhErrSbrx=`$command`;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-1070- # --------------------------------------------------
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-6267-# print $fhoutSbr "--- $sbrName3: system '$cmd'\n" if ($fhoutSbr);
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl:6268:# system("$cmd");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/formats.pl-6269-# }
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/hssp.pl-436- $cmd="\\mv $filetmp $fileInLoc";
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/hssp.pl:437: system($cmd);
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/hssp.pl-438- print "--- $sbrName: system '$cmd'\n"
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/scr.pl-1485- $scr=$exePvmgetarch;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/scr.pl:1486: $archFound=`$scr`; # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/scr.pl-1487- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/scr.pl-1517- $scr=$exePvmgetarch;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/scr.pl:1518: $archFound=`$scr`; # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/lib/scr.pl-1519- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-2270- if ($exeConv=~/\.pl/){
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm:2271: system("$exeConv $fileFssp $dirDsspLoc >> $fileDafTmp"); }
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-2272- # ------------------------------
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-4463- $scr=$exePvmgetarch;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm:4464: $archFound=`$scr`; # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-4465- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-4495- $scr=$exePvmgetarch;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm:4496: $archFound=`$scr`; # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-4497- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-4555- ($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm:4556: return(0,"*** ERROR $sbrName: failed to run system ($cmd)\n".$msg."\n")
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-4557- if (! $Lok || ! -e $fileTmpLoc);
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-7207- foreach $tmp(@tmp){
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm:7208: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/copf.pm-7209- last;}}
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-1722- $scr=$exePvmgetarch;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm:1723: $archFound=`$scr`; # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-1724- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-1754- $scr=$exePvmgetarch;
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm:1755: $archFound=`$scr`; # system call
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-1756- $archFound=~s/\s|\n//g;
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-2597-
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm:2598: $Lok= system("$niceLoc \\cp $fileToCopy $fileToCopyTo");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-2599-# return(0,"*** $sbrName: fail copy '$fileToCopy -> $fileToCopyTo' ($Lok)!") if (! $Lok);
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-2621- foreach $tmp(@tmp){
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm:2622: if (-e $tmp){$Lok=require("$tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/embl/scr/pack/hssp_filter.pm-2623- last;}}
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-635-# $par{"dirOut"},"'\n" if (! $Lok);
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl:636: system( @cmd ) && Carp::confess( "@cmd failed: ".( $? >> 8 ) );
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-637- print "--- $sbrName system '@cmd'\n" if ($par{"verb2"});
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-667- my @cmd = ( "mkdir", '-p', '-m', '0755', $tmp );
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl:668: system( @cmd ) && Carp::confess( "@cmd failed: ".( $? >> 8 ) );
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-669- print "--- $sbrName system '@cmd'\n" if ($par{"verb2"});
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-3333-
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl:3334: $Lok= system("\\cp $fileToCopy $fileToCopyTo");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-3335- if( $Lok ){ Carp::confess( "cmd \\cp $fileToCopy $fileToCopyTo failed: ".( $? >> 8 ) ); }
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-3375- $Lok=
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl:3376: require($exe_ctime)
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-col.pl-3377- if (-e $exe_ctime); }
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl-529- if (length($errMsg)>1){
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl:530: system ("echo '$fileInLoc' >> ".$par{"fileOutErrorBlast"});
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl-531- $msg="*** ERROR $SBR3: FATAL problem BLAST input mat=".
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl-9550- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl:9551:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl:9552: system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl-9553- }
##############################################
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl-10379-# prot2nn_seqLocSalt sums over salt bridges to [ED]-[KL]=1, [KL]-[ED]=1
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl:10380:# i,(i+n) where n=1..$winLoc
profphd-1.0.42/.pc/1_remove_defined_array.patch/src/prof/scr/lib/lib-prof.pl-10381-# NOTE: =1 if either i-n OR i+n opposite charge
##############################################
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl-529- if (length($errMsg)>1){
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl:530: system ("echo '$fileInLoc' >> ".$par{"fileOutErrorBlast"});
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl-531- $msg="*** ERROR $SBR3: FATAL problem BLAST input mat=".
##############################################
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl-9550- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl:9551:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl:9552: system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl-9553- }
##############################################
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl-10379-# prot2nn_seqLocSalt sums over salt bridges to [ED]-[KL]=1, [KL]-[ED]=1
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl:10380:# i,(i+n) where n=1..$winLoc
profphd-1.0.42/.pc/3_fix_indexing.patch/src/prof/scr/lib/lib-prof.pl-10381-# NOTE: =1 if either i-n OR i+n opposite charge
##############################################
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl-529- if (length($errMsg)>1){
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl:530: system ("echo '$fileInLoc' >> ".$par{"fileOutErrorBlast"});
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl-531- $msg="*** ERROR $SBR3: FATAL problem BLAST input mat=".
##############################################
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl-9550- $tmp2{"len"},$tmp2{"nhtm"},$tmp2{"aveLenHtm"});
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl:9551:# system("echo '$tmpWrt' >> stat-htm-glob.tmp");
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl:9552: system("echo '$tmpWrt' >> stat-htm-htm.tmp");
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl-9553- }
##############################################
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl-10379-# prot2nn_seqLocSalt sums over salt bridges to [ED]-[KL]=1, [KL]-[ED]=1
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl:10380:# i,(i+n) where n=1..$winLoc
profphd-1.0.42/.pc/4_fix_negative_repeat_count.patch/src/prof/scr/lib/lib-prof.pl-10381-# NOTE: =1 if either i-n OR i+n opposite charge