       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