diff mayachemtools/bin/SortSDFiles.pl @ 0:73ae111cf86f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/bin/SortSDFiles.pl	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,400 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: SortSDFiles.pl,v $
+# $Date: 2015/02/28 20:46:21 $
+# $Revision: 1.26 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use FindBin; use lib "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use SDFileUtil;
+use TextUtil;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Get the options and setup script...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+my(@SDFilesList);
+@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
+
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+print "Checking input SD file(s)...\n";
+my(%SDFilesInfo);
+RetrieveSDFilesInfo();
+
+# Generate output files...
+my($FileIndex);
+if (@SDFilesList > 1) {
+  print "\nProcessing SD files...\n";
+}
+for $FileIndex (0 .. $#SDFilesList) {
+  if ($SDFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $SDFilesList[$FileIndex]...\n";
+    SortSDFile($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Sort it out...
+sub SortSDFile {
+  my($Index) = @_;
+  my($SDFile, $NewSDFile, $KeyDataFieldName);
+
+  $SDFile = $SDFilesList[$Index];
+  $NewSDFile = $SDFilesInfo{OutFile}[$Index];
+  $KeyDataFieldName = $SDFilesInfo{KeyDataFieldName}[$Index];
+
+  print "Generating new SD file $NewSDFile...\n";
+  open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
+  open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
+
+  # Go over all compound records and store 'em using key value as hash...
+  my(%KeyToCompundRecordsMap, @InvalidCompoundRecords, $CmpdCount, $CmpdString, @CmpdLines, %DataFieldValues, $KeyDataFieldValue);
+  %KeyToCompundRecordsMap = ();
+  @InvalidCompoundRecords = ();
+  $CmpdCount = 0;
+
+  COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
+      $CmpdCount++;
+      @CmpdLines = split "\n", $CmpdString;
+      %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+      #Make sure data field value is okay...
+      if (!(IsNotEmpty($DataFieldValues{$KeyDataFieldName}) && ($DataFieldValues{$KeyDataFieldName} !~ /\n/))) {
+	push @InvalidCompoundRecords, $CmpdString;
+	if ($OptionsInfo{DetailLevel} >= 3 ) {
+	  print "Ignoring compound record $CmpdCount: Contains empty value for key data field $KeyDataFieldName :\n $CmpdString\n\n";
+	}
+	elsif ($OptionsInfo{DetailLevel} >= 2) {
+	  print "Ignoring compound record $CmpdCount: Contains empty value for key data field $KeyDataFieldName...\n";
+	}
+	next COMPOUND;
+      }
+      $KeyDataFieldValue = $DataFieldValues{$KeyDataFieldName};
+      if ($OptionsInfo{KeyData} =~ /^numeric$/i) {
+	if (!IsFloat($KeyDataFieldValue)) {
+	  push @InvalidCompoundRecords, $CmpdString;
+	  if ($OptionsInfo{DetailLevel} >= 3 ) {
+	    print "Ignoring compound record $CmpdCount: Contains non-numerical value for key data field $KeyDataFieldName :\n $CmpdString\n\n";
+	  }
+	  elsif ($OptionsInfo{DetailLevel} >= 2) {
+	    print "Ignoring compound record $CmpdCount: Contains non-numerical value for key data field $KeyDataFieldName...\n";
+	  }
+	  next COMPOUND;
+	}
+      }
+      if (exists($KeyToCompundRecordsMap{$KeyDataFieldValue})) {
+	# Append to existing coompund data...
+	$KeyToCompundRecordsMap{$KeyDataFieldValue} .= "\n" . $CmpdString;
+      }
+      else {
+	$KeyToCompundRecordsMap{$KeyDataFieldValue} = $CmpdString;
+      }
+  }
+
+  if ($OptionsInfo{Sort} =~ /^ascending$/i) {
+    if ($OptionsInfo{KeyData} =~ /^alphanumeric$/i) {
+      for $KeyDataFieldValue (sort { lc($a) cmp lc($b) } keys %KeyToCompundRecordsMap ) {
+	print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
+      }
+    }
+    else {
+      for $KeyDataFieldValue (sort { $a <=> $b } keys %KeyToCompundRecordsMap ) {
+	print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
+      }
+    }
+  }
+  else {
+    if ($OptionsInfo{KeyData} =~ /^alphanumeric$/i) {
+      for $KeyDataFieldValue (sort { lc($b) cmp lc($a) } keys %KeyToCompundRecordsMap ) {
+	print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
+      }
+    }
+    else {
+      for $KeyDataFieldValue (sort { $b <=> $a } keys %KeyToCompundRecordsMap ) {
+	print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
+      }
+    }
+  }
+  # Append the records containing data not appropriate for sorting...
+  if (@InvalidCompoundRecords) {
+    print "Placing ", scalar(@InvalidCompoundRecords)," compound record(s) with invalid data field key data the end...\n";
+    for $CmpdString (@InvalidCompoundRecords) {
+      print NEWSDFILE "$CmpdString\n";
+    }
+  }
+  close NEWSDFILE;
+  close SDFILE;
+}
+
+# Retrieve information about input SD files...
+sub RetrieveSDFilesInfo {
+  my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $DataFieldName);
+
+  %SDFilesInfo = ();
+
+  @{$SDFilesInfo{FileOkay}} = ();
+  @{$SDFilesInfo{OutFile}} = ();
+  @{$SDFilesInfo{KeyDataFieldName}} = ();
+
+  FILELIST: for $Index (0 .. $#SDFilesList) {
+    $SDFile = $SDFilesList[$Index];
+    $SDFilesInfo{FileOkay}[$Index] = 0;
+    $SDFilesInfo{OutFile}[$Index] = "";
+    $SDFilesInfo{KeyDataFieldName}[$Index] = "";
+
+    if (!(-e $SDFile)) {
+      warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($SDFile, "sd sdf")) {
+      warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
+      next FILELIST;
+    }
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
+    if ($Options{root} && (@SDFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$FileName = $RootFileName;
+      }
+      else {
+	$FileName = $Options{root};
+      }
+      $OutFileRoot = $FileName;
+    }
+    else {
+      $OutFileRoot = $FileName . "SortedByDataField";
+    }
+
+    $OutFile = $OutFileRoot . ".$FileExt";
+    if (lc($OutFile) eq lc($SDFile)) {
+      warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
+      next FILELIST;
+    }
+    if (!$Options{overwrite}) {
+      if (-e $OutFile) {
+	warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
+	next FILELIST;
+      }
+    }
+    # Setup data field name...
+    if ($OptionsInfo{SpecifiedDataFieldName}) {
+      $DataFieldName = $OptionsInfo{SpecifiedDataFieldName};
+    }
+    else {
+      my($CmpdString, @CmpdLines, @DataFieldNames);
+      @DataFieldNames = ();
+      if (!open(SDFILE, "$SDFile")) {
+	warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
+	next FILELIST;
+      }
+      $CmpdString = ReadCmpdString(\*SDFILE);
+      close SDFILE;
+
+      @CmpdLines = split "\n", $CmpdString;
+      @DataFieldNames = GetCmpdDataHeaderLabels(\@CmpdLines);
+      $DataFieldName = $DataFieldNames[0];
+    }
+
+    $SDFilesInfo{FileOkay}[$Index] = 1;
+    $SDFilesInfo{OutFile}[$Index] = "$OutFile";
+    $SDFilesInfo{KeyDataFieldName}[$Index] = $DataFieldName;
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  $OptionsInfo{DetailLevel} = $Options{detail};
+
+  $OptionsInfo{Key} = defined $Options{key} ? $Options{key} : undef;
+  $OptionsInfo{SpecifiedDataFieldName} = "";
+  if (defined $Options{key}) {
+    $OptionsInfo{SpecifiedDataFieldName} = $Options{key};
+  }
+
+  $OptionsInfo{KeyData} = $Options{keydata};
+  $OptionsInfo{Sort} = $Options{sort};
+
+  $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+  $OptionsInfo{Root} = defined $Options{root} ? $Options{root} : undef;
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{detail} = 1;
+  $Options{sort} = "ascending";
+  $Options{keydata} = "numeric";
+  if (!GetOptions(\%Options, "detail|d=i", "help|h",  "key|k=s", "keydata=s", "overwrite|o", "root|r=s", "sort|s=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
+  }
+  if ($Options{workingdir}) {
+    if (! -d $Options{workingdir}) {
+      die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
+    }
+    chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
+  }
+  if ($Options{keydata} !~ /^(numeric|alphanumeric)$/i) {
+    die "Error: The value specified, $Options{keydata}, for option \"--keydata\" is not valid. Allowed values: numeric or alphanumeric\n";
+  }
+  if ($Options{sort} !~ /^(ascending|descending)$/i) {
+    die "Error: The value specified, $Options{sort}, for option \"-s --sort\" is not valid. Allowed values: ascending or descending\n";
+  }
+  if (!IsPositiveInteger($Options{detail})) {
+    die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+SortSDFiles.pl - Sort SDFile(s) using values for a data field
+
+=head1 SYNOPSIS
+
+SortSDFiles.pl SDFile(s)...
+
+SortSDFiles.pl [B<-d, --detail> infolevel] [B<-h, --help>] [B<-k, --key> I<SD data field name>]
+[B<--keydata> numeric | alphanumeric] [B<-o, --overwrite>] [B<-r, --root> rootname]
+[B<-s, --sort> ascending | descending] [B<-w, --workingdir> dirname] SDFile(s)...
+
+=head1 DESCRIPTION
+
+Sort I<SDFile(s)> using values for a specified data field name key. Only one SD
+data field name key can be specified for sorting. In an event of conflict during sorting
+process, two similar values for a SD data field name key are simply transferred to
+output files in order of their presence in input files. Additionally, compound records
+with no data field name, empty field values, or field values containing multiple lines
+are simply placed at the end. The file names are separated by space.The valid file
+extensions are I<.sdf> and I<.sd>. All other file names are ignored. All the SD files in a
+current directory can be specified either by I<*.sdf> or the current directory name.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-d, --detail> I<infolevel>
+
+Level of information to print about compound records being ignored. Default: I<1>. Possible
+values: I<1, 2 or 3>.
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<-k, --key> I<SD data field name>
+
+I<SDFile(s)> data field name used for sorting compound records. Default value: I<first
+data field name>. Compound records with no I<sdfieldname>, empty field values, field
+values containing multiple lines, or field values inappropriate for sorting are simply placed
+at the end.
+
+=item B<--keydata> I<numeric | alphanumeric>
+
+Data type for I<sdfieldname> values. Possible values: I<numeric or alphanumeric>. Default
+value: I<numeric>. For I<alphanumeric> data values, comparison is case insensitive.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-r, --root> I<rootname>
+
+New SD file name is generated using the root: <Root>.<Ext>. Default new file
+name: <InitialSDFileName>SortedByDataField.<Ext>. This option is ignored for multiple
+input files.
+
+=item B<-s, --sort> I<ascending | descending>
+
+Sorting order for SD data field values. Possible values: I<ascending or descending>.
+Default value: I<ascending>.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To perform numerical sort in ascending order using first data field values and
+generate a new SD file NewSample1.sdf, type:
+
+    % SortSDFiles.pl -o -r NewSample1 Sample1.sdf
+
+To perform numerical sort in descending order using MolWeight data field and
+generate a new SD text file NewSample1.sdf, type:
+
+    % SortSDFiles.pl -k MolWeight --keydata numeric -s descending
+      -r NewSample1 -o Sample1.sdf
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+JoinSDFiles.pl, MergeTextFilesWithSD.pl, SplitSDFiles.pl, SDFilesToHTML.pl
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut