Mercurial > repos > deepakjadmin > r_caret_test
diff mayachemtool/mayachemtools/bin/ModifyTextFilesFormat.pl @ 0:68300206e90d draft default tip
Uploaded
author | deepakjadmin |
---|---|
date | Thu, 05 Nov 2015 02:41:30 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtool/mayachemtools/bin/ModifyTextFilesFormat.pl Thu Nov 05 02:41:30 2015 -0500 @@ -0,0 +1,331 @@ +#!/usr/bin/perl -w +# +# $RCSfile: ModifyTextFilesFormat.pl,v $ +# $Date: 2015/02/28 20:46:20 $ +# $Revision: 1.34 $ +# +# Author: Manish Sud <msud@san.rr.com> +# +# 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"); + +# Process options... +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"; + ModifyTextFileFormat($FileIndex); + } +} +print "\n$ScriptName:Done...\n\n"; + +$EndTime = new Benchmark; +$TotalTime = timediff ($EndTime, $StartTime); +print "Total time: ", timestr($TotalTime), "\n"; + +############################################################################### + +# Modify text file format... +sub ModifyTextFileFormat { + my($Index) = @_; + my($TextFile, $NewTextFile, $InDelim, $Line, @Words); + + $TextFile = $TextFilesList[$Index]; + + $NewTextFile = $TextFilesInfo{OutFile}[$Index]; + $InDelim = $TextFilesInfo{InDelim}[$Index]; + + print "Generating new $NewTextFile file...\n"; + + open NEWTEXTFILE, ">$NewTextFile" or die "Error: Can't open $NewTextFile !$ \n"; + open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n"; + + while ($Line = GetTextLine(\*TEXTFILE)) { + @Words = quotewords($InDelim, 0, $Line); + $Line = JoinWords(\@Words, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); + print NEWTEXTFILE "$Line\n"; + } + + close NEWTEXTFILE; + close TEXTFILE; +} + +# Retrieve information about input text files... +sub RetrieveTextFilesInfo { + my($Index, $TextFile, $NewTextFile, $FileDir, $FileName, $FileExt, $InDelim, $OutFileExt); + + %TextFilesInfo = (); + @{$TextFilesInfo{FileOkay}} = (); + @{$TextFilesInfo{InDelim}} = (); + @{$TextFilesInfo{OutFile}} = (); + + FILELIST: for $Index (0 .. $#TextFilesList) { + $TextFile = $TextFilesList[$Index]; + + $TextFilesInfo{FileOkay}[$Index] = 0; + $TextFilesInfo{InDelim}[$Index] = ""; + $TextFilesInfo{OutFile}[$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 $TextFile: It's not a csv or tsv file\n"; + next FILELIST; + } + if (!open TEXTFILE, "$TextFile") { + warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n"; + next FILELIST; + } + close TEXTFILE; + + ($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) { + $InDelim = "\;"; + } + } + + if (lc($InDelim) eq lc($OptionsInfo{OutDelim})) { + warn "Warning: Ignoring file $TextFile: The value specified, $Options{outdelim}, for option \"--outdelim\" is same as input delimiter\n"; + next FILELIST; + } + + $OutFileExt = ($Options{outdelim} =~ /^tab$/i ) ? "tsv" : "csv"; + + $NewTextFile = $FileName; + if ($OptionsInfo{OutFileRoot} && (@TextFilesList == 1)) { + my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); + if ($RootFileName && $RootFileExt) { + $NewTextFile = $RootFileName; + } + else { + $NewTextFile = $OptionsInfo{OutFileRoot}; + } + $NewTextFile .= ".$OutFileExt"; + } + else { + $NewTextFile .= "FormatModified" . ".$OutFileExt"; + } + + if (!$OptionsInfo{Overwrite}) { + if (-e $NewTextFile) { + warn "Warning: Ignoring file $TextFile: New Text file, $NewTextFile, already exists\n"; + next FILELIST; + } + } + + $TextFilesInfo{FileOkay}[$Index] = 1; + $TextFilesInfo{InDelim}[$Index] = $InDelim; + $TextFilesInfo{OutFile}[$Index] = $NewTextFile; + } + +} + +# Process option values... +sub ProcessOptions { + %OptionsInfo = (); + + $OptionsInfo{InDelim} = $Options{indelim}; + + $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; + +} + +# Setup script usage and retrieve command line arguments specified using various options... +sub SetupScriptUsage { + + # Retrieve all the options... + %Options = (); + + $Options{indelim} = "comma"; + $Options{outdelim} = "tab"; + $Options{quote} = "yes"; + + if (!GetOptions(\%Options, "help|h", "indelim=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "workingdir|w=s")) { + die "\nTo get a list of valid options and their values, use \"$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"; + } +} + +__END__ + +=head1 NAME + +ModifyTextFilesFormat.pl - Change CSV Textfile(s) into TSV Textfile(s) and vice versa + +=head1 SYNOPSIS + +ModifyTextFilesFormat.pl TextFile(s)... + +ModifyTextFilesFormat.pl [B<-h, --help>] [B<--indelim> comma | semicolon] +[B<--outdelim> comma | tab | semicolon] [B<-q, --quote> yes | no] [B<-r, --root> rootname] +[B<-w, --workingdir> dirname] TextFile(s)... + +=head1 DESCRIPTION + +Interchange CSV and TSV I<TextFile(s)> format. Mutiple 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<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<-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 new file +name: <InitialTextFileName>FormatModified.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files +respectively. 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 convert Sample*.csv into TSV files, type: + + % ModifyTextFilesFormat.pl --outdelim tab -q no -o Sample*.csv + +To convert Sample1.tsv into NewSample1.csv without any quotes around column +data values, type: + + % ModifyTextFilesFormat.pl --outdelim comma - q no + -r NewSample1 -o Sample1.tsv + +=head1 AUTHOR + +Manish Sud <msud@san.rr.com> + +=head1 SEE ALSO + +ModifyNewLineChar.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