1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: JoinSDFiles.pl,v $ 4 # $Date: 2015/02/28 20:46:20 $ 5 # $Revision: 1.35 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2015 Manish Sud. All rights reserved. 10 # 11 # This file is part of MayaChemTools. 12 # 13 # MayaChemTools is free software; you can redistribute it and/or modify it under 14 # the terms of the GNU Lesser General Public License as published by the Free 15 # Software Foundation; either version 3 of the License, or (at your option) any 16 # later version. 17 # 18 # MayaChemTools is distributed in the hope that it will be useful, but without 19 # any warranty; without even the implied warranty of merchantability of fitness 20 # for a particular purpose. See the GNU Lesser General Public License for more 21 # details. 22 # 23 # You should have received a copy of the GNU Lesser General Public License 24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or 25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, 26 # Boston, MA, 02111-1307, USA. 27 # 28 29 use strict; 30 use FindBin; use lib "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Benchmark; 34 use SDFileUtil; 35 use FileUtil; 36 37 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 38 39 # Autoflush STDOUT 40 $| = 1; 41 42 # Starting message... 43 $ScriptName = basename $0; 44 print "\n$ScriptName:Starting...\n\n"; 45 $StartTime = new Benchmark; 46 47 # Get the options and setup script... 48 SetupScriptUsage(); 49 if ($Options{help} || @ARGV < 1) { 50 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 51 } 52 53 my(@SDFilesList); 54 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); 55 if (@SDFilesList == 1) { 56 die "Error: Specify more than one SD file.\n"; 57 } 58 59 # Process options... 60 print "Processing options...\n"; 61 my(%OptionsInfo); 62 ProcessOptions(); 63 64 # Setup information about input files... 65 print "Checking input SD files...\n"; 66 my(%SDFilesInfo); 67 RetrieveSDFilesInfo(); 68 69 # Join files... 70 print "\nGenerating new SD file $OptionsInfo{NewSDFile}...\n"; 71 JoinSDFiles(); 72 73 print "\n$ScriptName:Done...\n\n"; 74 75 $EndTime = new Benchmark; 76 $TotalTime = timediff ($EndTime, $StartTime); 77 print "Total time: ", timestr($TotalTime), "\n"; 78 79 ############################################################################### 80 81 # Join all valid SD files... 82 sub JoinSDFiles { 83 my($FileIndex, $SDFile, $NewSDFile); 84 85 $NewSDFile = $OptionsInfo{NewSDFile}; 86 87 open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n"; 88 FILELIST: for $FileIndex (0 .. $#SDFilesList) { 89 if (!$SDFilesInfo{FileOkay}[$FileIndex]) { 90 next FILELIST; 91 } 92 $SDFile = $SDFilesList[$FileIndex]; 93 print "\nProcessing file $SDFile...\n"; 94 95 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n"; 96 while (<SDFILE>) { 97 s/(\r\n)|(\r)/\n/g; 98 print NEWSDFILE; 99 } 100 close SDFILE; 101 } 102 103 close NEWSDFILE; 104 } 105 106 # Retrieve information about SD files... 107 sub RetrieveSDFilesInfo { 108 my($Index, $SDFile); 109 110 %SDFilesInfo = (); 111 @{$SDFilesInfo{FileOkay}} = (); 112 113 FILELIST: for $Index (0 .. $#SDFilesList) { 114 $SDFilesInfo{FileOkay}[$Index] = 0; 115 116 $SDFile = $SDFilesList[$Index]; 117 if (!(-e $SDFile)) { 118 warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; 119 next FILELIST; 120 } 121 if (!CheckFileType($SDFile, "sdf sd")) { 122 warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; 123 next FILELIST; 124 } 125 if (! open SDFILE, "$SDFile") { 126 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n"; 127 next FILELIST; 128 } 129 close SDFILE; 130 131 $SDFilesInfo{FileOkay}[$Index] = 1; 132 } 133 } 134 135 # Process option values... 136 sub ProcessOptions { 137 my($FileDir, $FileName, $FileExt, $NewSDFile); 138 139 %OptionsInfo = (); 140 141 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : undef; 142 $OptionsInfo{Overwrite} = $Options{overwrite} ? $Options{overwrite} : undef; 143 144 if ($Options{root}) { 145 $FileDir = ""; $FileName = ""; $FileExt = ""; 146 ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root}); 147 if ($FileName && $FileExt) { 148 $NewSDFile = $FileName . "." . $FileExt; 149 } 150 else { 151 $NewSDFile = $Options{root} . ".sdf"; 152 } 153 } 154 else { 155 $FileDir = ""; $FileName = ""; $FileExt = ""; 156 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFilesList[0]); 157 $NewSDFile = $FileName . "1To" . @SDFilesList . "Joined.sdf"; 158 } 159 160 if (!$Options{overwrite}) { 161 if (-e $NewSDFile) { 162 die "Error: The file $NewSDFile already exists.\n"; 163 } 164 } 165 if ($Options{root}) { 166 my($FileIndex); 167 for $FileIndex (0 .. $#SDFilesList) { 168 if (lc($NewSDFile) eq lc($SDFilesList[$FileIndex])) { 169 die "Error: Output filename, $NewSDFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n"; 170 } 171 } 172 } 173 $OptionsInfo{NewSDFile} = $NewSDFile; 174 175 } 176 177 # Setup script usage and retrieve command line arguments specified using various options... 178 sub SetupScriptUsage { 179 180 # Retrieve all the options... 181 %Options = (); 182 if (!GetOptions(\%Options, "help|h", "overwrite|o", "root|r=s", "workingdir|w=s")) { 183 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 184 } 185 if ($Options{workingdir}) { 186 if (! -d $Options{workingdir}) { 187 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 188 } 189 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 190 } 191 } 192