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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/JoinTextFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,404 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: JoinTextFiles.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.32 $
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+
+my($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");
+
+if (@TextFilesList == 1) {
+  die "Error: Specify more than one Text file.\n";
+}
+
+# Process options...
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+# Setup information about input files...
+print "Checking input text files...\n";
+my(%TextFilesInfo);
+RetrieveTextFilesInfo();
+
+# Join files...
+print "\nGenerating new text file $OptionsInfo{NewTextFile}...\n";
+JoinTextFiles();
+
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Join all valid Text files...
+sub JoinTextFiles {
+  my($FileIndex, $TextFile, $NewTextFile, $Line, $FirstColLabelsLine, $OutDelim, $OutQuote, $InDelim, @Words, @ColLabels);
+
+  $NewTextFile = $OptionsInfo{NewTextFile};
+
+  $FirstColLabelsLine = '';
+
+  $OutDelim = $OptionsInfo{OutDelim}; $OutQuote = $OptionsInfo{OutQuote};
+
+  open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
+  FILELIST: for $FileIndex (0 .. $#TextFilesList) {
+    if (!$TextFilesInfo{FileOkay}[$FileIndex]) {
+      next FILELIST;
+    }
+
+    $TextFile = $TextFilesList[$FileIndex];
+    $InDelim = $TextFilesInfo{InDelim}[$FileIndex];
+
+    print "\nProcessing file $TextFile...\n";
+
+    open TEXTFILE, "$TextFile" or die "Error: Couldn't open $TextFile: $! \n";
+
+    if ($OptionsInfo{Label}) {
+      if ($OptionsInfo{Fast}) {
+	$Line = GetTextLine(\*TEXTFILE);
+	if (!$FirstColLabelsLine) {
+	  $FirstColLabelsLine = $Line;
+	  print NEWTEXTFILE "$FirstColLabelsLine\n";
+	}
+      }
+      else {
+	$Line = GetTextLine(\*TEXTFILE);
+	if (!$FirstColLabelsLine) {
+	  @ColLabels = quotewords($InDelim, 0, $Line);
+	  $FirstColLabelsLine = JoinWords(\@ColLabels, $OutDelim, $OutQuote);
+	  print NEWTEXTFILE "$FirstColLabelsLine\n";
+	}
+      }
+    }
+
+    while ($Line = GetTextLine(\*TEXTFILE)) {
+      if (!$OptionsInfo{Fast}) {
+	@Words = quotewords($InDelim, 0, $Line);
+	$Line = JoinWords(\@Words, $OutDelim, $OutQuote);
+      }
+      print NEWTEXTFILE "$Line\n";
+    }
+    close TEXTFILE;
+  }
+
+  close NEWTEXTFILE;
+}
+
+# Retrieve information about Text files...
+sub RetrieveTextFilesInfo {
+  my($Index, $TextFile, $InDelim, $Line, $FirstColLabelsLine, $ColLabelsLine, $FileDir, $FileName, $FileExt, @FirstColLabels, @ColLabels);
+
+  %TextFilesInfo = ();
+  @{$TextFilesInfo{FileOkay}} = ();
+  @{$TextFilesInfo{InDelim}} = ();
+
+  $FirstColLabelsLine = ''; $ColLabelsLine = '';
+  @FirstColLabels = (); @ColLabels = ();
+
+  FILELIST: for $Index (0 .. $#TextFilesList) {
+    $TextFilesInfo{FileOkay}[$Index] = 0;
+    $TextFilesInfo{InDelim}[$Index] = "";
+
+    $TextFile = $TextFilesList[$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 $TextFile: It's not a Text file\n";
+      next FILELIST;
+    }
+
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
+    if ($FileExt =~ /^tsv$/i) {
+      $InDelim = "\t";
+    }
+    else {
+      $InDelim = "\,";
+      if ($OptionsInfo{InDelim} !~ /^(comma|semicolon)$/i) {
+	warn "Warning: Ignoring file $TextFile: The value specified, $OptionsInfo{InDelim}, for option \"--indelim\" is not valid for csv files\n";
+	next FILELIST;
+      }
+      if ($OptionsInfo{InDelim} =~ /^semicolon$/i) {
+	$InDelim = "\;";
+      }
+    }
+
+    if (! open TEXTFILE, "$TextFile") {
+      warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    $Line = GetTextLine(\*TEXTFILE);
+    close TEXTFILE;
+
+    if ($OptionsInfo{Label}) {
+      if (!$OptionsInfo{Fast}) {
+	@ColLabels = quotewords($InDelim, 0, $Line);
+	if ($FirstColLabelsLine) {
+	  if (@ColLabels != @FirstColLabels) {
+	    warn "Warning: Ignoring file $TextFile: The number of columns in this file, ", scalar(@ColLabels), ", is different from the number of columns, ", scalar(@FirstColLabels), ", in the first valid text file. \n";
+	    next FILELIST;
+	  }
+	  $ColLabelsLine = JoinWords(\@ColLabels, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+	  if ($ColLabelsLine ne $FirstColLabelsLine) {
+	    warn "Warning: Ignoring file $TextFile: The column names in this file are different from those in first valid text file.\nColumnlabels in first valid text file: $FirstColLabelsLine \nColumnlabels in current text file: $ColLabelsLine\n";
+	    next FILELIST;
+	  }
+	}
+	else {
+	  @FirstColLabels = @ColLabels;
+	  $FirstColLabelsLine = JoinWords(\@FirstColLabels, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+	}
+      }
+    }
+
+    $TextFilesInfo{FileOkay}[$Index] = 1;
+    $TextFilesInfo{InDelim}[$Index] = $InDelim;
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  my($FileDir, $FileName, $FileExt, $NewTextFile, $Index);
+
+  %OptionsInfo = ();
+
+  $OptionsInfo{Fast} = $Options{fast} ? $Options{fast} : 0;
+
+  $OptionsInfo{InDelim} = $Options{indelim};
+  $OptionsInfo{Label} = ($Options{label} =~ /^yes$/i) ? 1 : 0;
+
+  $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : undef;
+  $OptionsInfo{Overwrite} = $Options{overwrite} ? $Options{overwrite} : undef;
+
+  $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
+  $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
+
+  if ($Options{root}) {
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root});
+    if ($FileName && $FileExt) {
+      $NewTextFile = $FileName;
+    }
+    else {
+      $NewTextFile =  $Options{root};
+    }
+  }
+  else {
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFilesList[0]);
+    $NewTextFile = $FileName . "1To" . @TextFilesList . "Joined";
+  }
+
+  if ($Options{outdelim} =~ /^tab$/i) {
+    $NewTextFile .= ".tsv";
+  }
+  else {
+    $NewTextFile .= ".csv";
+  }
+
+  if (!$Options{overwrite}) {
+    if (-e $NewTextFile) {
+      die "Error: The file $NewTextFile already exists.\n";
+    }
+  }
+
+  if ($Options{root}) {
+    for $Index (0 .. $#TextFilesList) {
+      if (lc($NewTextFile) eq lc($TextFilesList[$Index])) {
+	die "Error: Output filename, $NewTextFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n";
+      }
+    }
+  }
+
+  $OptionsInfo{NewTextFile} = $NewTextFile;
+}
+
+# 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";
+  $Options{outdelim} = "comma";
+  $Options{quote} = "yes";
+  if (!GetOptions(\%Options, "fast|f", "help|h", "indelim=s", "label|l=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{outdelim} !~ /^(comma|semicolon|tab)$/i) {
+    die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
+  }
+  if ($Options{quote} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($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
+
+JoinTextFiles.pl - Join multiple CSV or TSV text files into a single text file
+
+=head1 SYNOPSIS
+
+JoinTextFiles.pl TextFiles...
+
+JoinTextFiles.pl  [B<-f, --fast>] [B<-h, --help>] [B<--indelim> comma | semicolon]
+[B<-l, --label> yes | no] [B<-o, --overwrite>] [B<--outdelim> comma | tab | semicolon]
+[B<-q, --quote> yes | no] [B<-r, --root> rootname] [B<-w, --workingdir> dirname] TextFiles...
+
+=head1 DESCRIPTION
+
+Multiple CSV or TSV I<TextFiles> are joined to generate a single text file. The
+file names are separated by spaces. 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<TextFiles>. Any file which doesn't correspond to the format indicated
+by B<--indelim> option is ignored.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-f, --fast>
+
+In this mode, B<--indelim> and B<-q --quote> options are ignored. The format of
+input and output file(s) are assumed to be similar. And the text lines from I<TextFiles>
+are simply transferred to output file without any processing.
+
+=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>.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<--outdelim> I<comma | tab | semicolon>
+
+Output text file delimiter. Possible values: I<comma, tab, or semicolon>
+Default value: I<comma>.
+
+=item B<-q, --quote> I<yes | no>
+
+Put quotes around column values in output text file. Possible values: I<yes or
+no>. Default value: I<yes>.
+
+=item B<-r, --root> I<rootname>
+
+New text file name is generated using the root: <Root>.<Ext>. Default file
+name: <FirstTextFileName>1To<Count>Joined.<Ext>. The csv, and tsv
+<Ext> values are used for comma/semicolon, and tab delimited text files
+respectively.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To join CSV text files, type:
+
+    % JoinTextFiles.pl -o Sample1.csv Sample2.csv
+    % JoinTextFiles.pl -o *.csv
+
+To join Sample*.tsv TSV text files into a NewSample.tsv file, type:
+
+    % JoinTextFiles.pl -o -r NewSample Sample*.tsv
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+MergeTextFiles.pl, ModifyTextFilesFormat.pl, SplitTextFiles.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