diff bin/TextFilesToSDFiles.pl @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/TextFilesToSDFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,348 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: TextFilesToSDFiles.pl,v $
+# $Date: 2015/02/28 20:46:21 $
+# $Revision: 1.25 $
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use SDFileUtil;
+
+my($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(@TextFilesList);
+@TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
+
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+print "Checking input text file(s)...\n";
+my(%TextFilesInfo);
+RetrieveTextFilesInfo();
+
+# Generate output files...
+my($FileIndex);
+if (@TextFilesList > 1) {
+  print "\nProcessing text files...\n";
+}
+for $FileIndex (0 .. $#TextFilesList) {
+  if ($TextFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $TextFilesList[$FileIndex]...\n";
+    ConvertTextFile($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Convert text file to SD file...
+sub ConvertTextFile {
+  my($Index) = @_;
+  my($TextFile, $SDFile, $Line, $InDelim, $Label, $Value, $ColIndex, $ColCount, @ColLabels, @LineWords);
+
+  $TextFile = $TextFilesList[$Index];
+  $InDelim = $TextFilesInfo{InDelim}[$Index];
+  $SDFile = $TextFilesInfo{OutSDFile}[$Index];
+  @ColLabels = @{$TextFilesInfo{ColLabels}[$Index]};
+  $ColCount = @ColLabels;
+
+  print "Generating SD file $SDFile...\n";
+  open SDFILE, ">$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
+  open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n";
+  if ($OptionsInfo{ColLabelsPresent}) {
+    # Skip over column labels from old file...
+    $Line = GetTextLine(\*TEXTFILE);
+  }
+  my($Date) = GenerateMiscLineDateStamp();
+  while ($Line = GetTextLine(\*TEXTFILE)) {
+    @LineWords = quotewords($InDelim, 0, $Line);
+
+    # Write out empty CTAB block...
+    print SDFILE GenerateEmptyCtabBlockLines($Date), "\n";
+
+    # Write out data fields and values...
+    for $ColIndex (0 .. $#LineWords) {
+      if ($ColIndex < $ColCount) {
+	$Label = $ColLabels[$ColIndex];
+	$Value = $LineWords[$ColIndex];
+	print SDFILE "> <$Label>\n$Value\n\n";
+      }
+    }
+    print SDFILE "\$\$\$\$\n";
+  }
+  close SDFILE;
+  close TEXTFILE;
+}
+
+# Retrieve information about input text files...
+sub RetrieveTextFilesInfo {
+  my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, @LineWords, @ColLabels, $OutFileRoot,  $OutFile, $ColNum, $ColLabel);
+
+  %TextFilesInfo = ();
+
+  @{$TextFilesInfo{FileOkay}} = ();
+  @{$TextFilesInfo{ColCount}} = ();
+  @{$TextFilesInfo{ColLabels}} = ();
+  @{$TextFilesInfo{InDelim}} = ();
+  @{$TextFilesInfo{OutSDFile}} = ();
+
+
+  FILELIST: for $Index (0 .. $#TextFilesList) {
+    $TextFile = $TextFilesList[$Index];
+
+    $TextFilesInfo{FileOkay}[$Index] = 0;
+    $TextFilesInfo{ColCount}[$Index] = 0;
+    $TextFilesInfo{InDelim}[$Index] = "";
+    $TextFilesInfo{OutSDFile}[$Index] = "";
+
+    @{$TextFilesInfo{ColLabels}[$Index]} = ();
+
+    if (!(-e $TextFile)) {
+      warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($TextFile, "csv tsv")) {
+      warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
+      next FILELIST;
+    }
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
+    if ($FileExt =~ /^tsv$/i) {
+      $InDelim = "\t";
+    }
+    else {
+      $InDelim = "\,";
+      if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
+	warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n";
+	next FILELIST;
+      }
+      if ($Options{indelim} =~ /^semicolon$/i) {
+	$InDelim = "\;";
+      }
+    }
+    if (!open TEXTFILE, "$TextFile") {
+      warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    $Line = GetTextLine(\*TEXTFILE);
+    @LineWords = quotewords($InDelim, 0, $Line);
+    @ColLabels = ();
+    if ($OptionsInfo{ColLabelsPresent}) {
+      push @ColLabels, @LineWords;
+    }
+    else {
+      for $ColNum (1 .. @LineWords) {
+	$ColLabel = "Column${ColNum}Data";
+	push @ColLabels, $ColLabel;
+      }
+    }
+    close TEXTFILE;
+
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
+    if ($Options{root} && (@TextFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$FileName = $RootFileName;
+      }
+      else {
+	$FileName = $Options{root};
+      }
+      $OutFileRoot = $FileName;
+    }
+    else {
+      $OutFileRoot = "${FileName}WithNoStrData";
+    }
+
+    $OutFile = "${OutFileRoot}.sdf";
+    if (!$Options{overwrite}) {
+      if (-e $OutFile) {
+	warn "Warning: Ignoring file $TextFile: The file $OutFile already exists\n";
+	next FILELIST;
+      }
+    }
+    $TextFilesInfo{FileOkay}[$Index] = 1;
+    $TextFilesInfo{InDelim}[$Index] = $InDelim;
+    $TextFilesInfo{OutSDFile}[$Index] = "$OutFile";
+
+    $TextFilesInfo{ColCount}[$Index] = @ColLabels;
+    push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  $OptionsInfo{Label} = $Options{label};
+  $OptionsInfo{ColLabelsPresent} = ($Options{label} =~ /^yes$/i) ? 1 : 0;
+
+  $OptionsInfo{InDelim} = $Options{indelim};
+  $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+
+  $OptionsInfo{OutFileRoot} = 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{label} = "yes";
+  $Options{indelim} = "comma";
+  if (!GetOptions(\%Options, "help|h", "indelim=s", "label|l=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{indelim} !~ /^(comma|semicolon)$/i) {
+    die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
+  }
+  if ($Options{label} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{label}, for option \"-l --label\" is not valid. Allowed values: yes or no\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+TextFilesToSDFiles.pl - Generate SD files from CSV or TSV TextFile(s)
+
+=head1 SYNOPSIS
+
+TextFilesToSDFiles.pl TextFile(s)...
+
+TextFilesToSDFiles.pl [B<-h, --help>] [B<--indelim> comma | semicolon] [B<-l, --label> yes | no]
+[B<-o, --overwrite>] [B<-r, --root> rootname] [B<-w, --workingdir> dirname] TextFile(s)...
+
+=head1 DESCRIPTION
+
+Generate SD files from CSV or TSV I<TextFile(s)>. The new SD files contain no structure data
+as indicated by empty structure data block; Data fields and values in SD files are generated
+using I<TextFile(s)> column labels and corresponding data values.
+
+Multiple I<TextFile(s)> names are separated by space. The valid file extensions are
+I<.csv> and I<.tsv> for comma/semicolon and tab delimited text files respectively.
+All other file names are ignored. All the text files in a current directory can be specified
+by I<*.csv>, I<*.tsv>, or the current directory name. The B<--indelim> option
+determines the format of I<TextFile(s)>. Any file which doesn't correspond to
+the format indicated by B<--indelim> option is ignored.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<--indelim> I<comma | semicolon>
+
+Input delimiter for CSV I<TextFile(s)>. Possible values: I<comma or semicolon>.
+Default value: I<comma>. For TSV files, this option is ignored and I<tab> is used as a
+delimiter.
+
+=item B<-l, --label> I<yes | no>
+
+First line contains column labels. Possible values: I<yes or no>. Default value: I<yes>.
+Column labels are used to create SD data field labels; otherwise, data field labels look
+like Column<colnumber>Data.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-r, --root> I<rootname>
+
+New SD file names are generated using the root: <Root>.sdf. Default new file names:
+<TextFileName>WithNoStrData.sdf. This option is ignored for multiple input files.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To generate NewSample1.sdf file from Sample1.csv file, type:
+
+    % TextFilesToSDFiles.pl -o -r NewSample1 Sample1.csv
+
+To generate NewSample1.sdf file from Sample1.tsv file which doesn't
+contain column labels line, type:
+
+    % TextFilesToSDFiles.pl --label no -o -r NewSample1 Sample1.tsv
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+JoinTextFiles.pl, MergeTextFiles.pl, ModifySDFilesDataFields.pl, ModifyTextFilesFormat.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