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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/InfoAminoAcids.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,635 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: InfoAminoAcids.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use AminoAcids;
+
+my($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}) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+ListAminoAcidProperties();
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# List data for an amino acid...
+sub ListAminoAcidData {
+  my($DataLabelRef, $DataValueRef) = @_;
+  my($Index, $Line, $Value);
+
+  if ($OptionsInfo{AminoAcidRowsOutput}) {
+    $Line = '';
+    # Format data...
+    if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) {
+      $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+    }
+    else {
+      # Always quote values containing commas...
+      $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0];
+      for $Index (1 .. $#{$DataValueRef} ) {
+	$Value = $DataValueRef->[$Index];
+	if ($Value =~ /\,/) {
+	  $Value = qq("$Value");
+	}
+	$Line .= $OptionsInfo{OutDelim} . $Value;
+      }
+    }
+    if ($OptionsInfo{FileOutput}) {
+      print OUTFILE "$Line\n";
+    }
+    else {
+      print "$Line\n";
+    }
+  }
+  else {
+    # Format and list data...
+    $Line = '';
+    for $Index (0 .. $#{$DataLabelRef} ) {
+      $Line = $DataLabelRef->[$Index] . ' ' . $DataValueRef->[$Index];
+      if ($OptionsInfo{FileOutput}) {
+	print OUTFILE "$Line\n";
+      }
+      else {
+	print "$Line\n";
+      }
+    }
+  }
+}
+
+# List data for an amino acid...
+sub ListHeaderRowData {
+  my($DataLabelRef) = @_;
+  my($Line);
+
+  # Format data...
+  $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+  $Line =~ s/\://g;
+  # List data...
+  if ($OptionsInfo{FileOutput}) {
+    print OUTFILE "$Line\n";
+  }
+  else {
+    print "$Line\n";
+  }
+}
+
+# List properties for amino acids...
+sub ListAminoAcidProperties {
+  my($AminoAcidID, $AminoAcidDataRef, $PropertyName, $PropertyValue, @PropertyLabels, @PropertyValues);
+
+  print "Listing information for amino acid(s)...\n";
+
+  if ($OptionsInfo{FileOutput}) {
+    print "Generating file $OptionsInfo{OutFileName}...\n";
+    open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n";
+  }
+
+  # Setup property labels...
+  @PropertyLabels = ();
+  for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
+    push @PropertyLabels, ("$PropertyName:");
+  }
+
+  if ($OptionsInfo{AminoAcidRowsOutput}) {
+    ListHeaderRowData(\@PropertyLabels);
+  }
+
+  # Go over specified properties...
+  for $AminoAcidID (@{$OptionsInfo{SpecifiedAminoAcidIDs}}) {
+    $AminoAcidDataRef = AminoAcids::GetAminoAcidPropertiesData($AminoAcidID);
+
+    if (!$OptionsInfo{AminoAcidRowsOutput}) {
+      if ($OptionsInfo{FileOutput}) {
+	print OUTFILE "\nListing properties for amino acid $AminoAcidID...\n\n";
+      }
+      else {
+	print "\nListing properties for amino acid $AminoAcidID...\n\n";
+      }
+    }
+
+    # Collect data..
+    @PropertyValues = ();
+    for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
+      $PropertyValue = $AminoAcidDataRef->{$PropertyName};
+      if (IsFloat($PropertyValue)) {
+	$PropertyValue = sprintf("%.$OptionsInfo{Precision}f", $PropertyValue) + 0;
+      }
+      push @PropertyValues, $PropertyValue;
+    }
+    # List data...
+    ListAminoAcidData(\@PropertyLabels, \@PropertyValues);
+  }
+  if ($OptionsInfo{FileOutput}) {
+    close OUTFILE;
+  }
+  print "\n";
+}
+
+# Get propery names from categories...
+sub GetPropertyNamesFromCategories {
+  my($CategoryName) = @_;
+  my(@PropertyNames);
+
+  @PropertyNames = ();
+  if ($CategoryName =~ /^Basic$/i) {
+    @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'ChemicalFormula','MolecularWeight', 'LinearStructure', 'LinearStructureAtpH7.4');
+  } elsif ($CategoryName =~ /^BasicPlus$/i) {
+    @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'AcidicBasic', 'PolarNonpolar', 'Charged', 'Aromatic', 'HydrophobicHydophilic', 'IsoelectricPoint', 'pKCOOH', 'pKNH3+', 'ChemicalFormula', 'MolecularWeight', 'ExactMass', 'ChemicalFormulaMinusH2O', 'MolecularWeightMinusH2O(18.01524)', 'ExactMassMinusH2O(18.01056)','LinearStructure', 'LinearStructureAtpH7.4');
+  } elsif ($CategoryName =~ /^BasicAndHydrophobicity$/i) {
+    @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'ChemicalFormula', 'MolecularWeight', 'LinearStructure', 'LinearStructureAtpH7.4', 'HydrophobicityEisenbergAndOthers', 'HydrophobicityHoppAndWoods', 'HydrophobicityJanin', 'HydrophobicityKyteAndDoolittle', 'HydrophobicityRoseAndOthers', 'HydrophobicityWolfendenAndOthers');
+  } elsif ($CategoryName =~ /^BasicAndHydrophobicityPlus$/i) {
+    @PropertyNames = ('ThreeLetterCode', 'OneLetterCode', 'AminoAcid', 'DNACodons', 'RNACodons', 'ChemicalFormula', 'MolecularWeight', 'LinearStructure', 'LinearStructureAtpH7.4', 'HydrophobicityAbrahamAndLeo', 'HydrophobicityBlack', 'HydrophobicityBullAndBreese', 'HydrophobicityChothia', 'HydrophobicityEisenbergAndOthers', 'HydrophobicityFauchereAndOthers', 'HydrophobicityGuy', 'HydrophobicityHPLCAtpH3.4Cowan', 'HydrophobicityHPLCAtpH7.5Cowan', 'HydrophobicityHPLCParkerAndOthers', 'HydrophobicityHPLCWilsonAndOthers', 'HydrophobicityHoppAndWoods', 'HydrophobicityJanin', 'HydrophobicityKyteAndDoolittle', 'HydrophobicityManavalanAndOthers', 'HydrophobicityMiyazawaAndOthers', 'HydrophobicityOMHSweetAndOthers', 'HydrophobicityRaoAndArgos', 'HydrophobicityRfMobility', 'HydrophobicityRoseAndOthers', 'HydrophobicityRoseman', 'HydrophobicityWellingAndOthers', 'HydrophobicityWolfendenAndOthers');
+  }
+
+  return @PropertyNames;
+}
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
+  $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
+
+  $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+  $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
+
+  $OptionsInfo{OutputStyle} = $Options{outputstyle};
+
+  $OptionsInfo{AminoAcidRowsOutput} = ($Options{outputstyle} =~ /^AminoAcidRows$/i) ? 1 : 0;
+  $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0;
+
+  $OptionsInfo{Precision} = $Options{precision};
+
+  my($AminoAcidID, @AminoAcidIDs);
+
+  @{$OptionsInfo{SpecifiedAminoAcidIDs}} = ();
+
+  # Set up Amino Acids IDs except for All mode...
+  @AminoAcidIDs = ();
+
+  if (@ARGV >= 1) {
+    push @AminoAcidIDs, @ARGV;
+  }
+  else {
+    # Setup mode specified default values...
+    push @AminoAcidIDs, 'Ala';
+  }
+
+  # Generate list of amino acids...
+  if (@ARGV == 1 && $ARGV[0] =~ /^All$/i) {
+    push @{$OptionsInfo{SpecifiedAminoAcidIDs}}, AminoAcids::GetAminoAcids();
+  }
+  else {
+    ID: for $AminoAcidID (@AminoAcidIDs) {
+      if (AminoAcids::IsAminoAcid($AminoAcidID)) {
+	push @{$OptionsInfo{SpecifiedAminoAcidIDs}}, $AminoAcidID;
+      }
+      else {
+	warn "Ignoring amino acid ID, $AminoAcidID, specified using command line parameter option: Unknown amino acid ID...\n";
+	next ID;
+      }
+    }
+  }
+  SetupSpecifiedProperties();
+
+  # Setup output file name...
+  $OptionsInfo{OutFileName} = '';
+  if ($OptionsInfo{FileOutput}) {
+    my($OutFileRoot, $OutFileExt);
+
+    $OutFileRoot = '';
+    $OutFileExt = "csv";
+    if ($Options{outdelim} =~ /^tab$/i) {
+      $OutFileExt = "tsv";
+    }
+    if ($Options{root}) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$OutFileRoot = $RootFileName;
+      }
+      else {
+	$OutFileRoot = $Options{root};
+      }
+    }
+    else {
+      $OutFileRoot = 'AminoAcidsInfo';
+    }
+    $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt;
+    if (!$Options{overwrite}) {
+      if (-e $OptionsInfo{OutFileName}) {
+	die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n";
+      }
+    }
+  }
+}
+
+# Setup properties to list...
+sub SetupSpecifiedProperties {
+
+  $OptionsInfo{Properties} = defined $Options{properties} ? $Options{properties} : undef;
+
+  $OptionsInfo{PropertiesMode} = $Options{propertiesmode};
+  $OptionsInfo{PropertiesListing} = $Options{propertieslisting};
+
+  # Make sure appropriate properties/category names are specified...
+  @{$OptionsInfo{SpecifiedProperies}} = ();
+  if ($Options{properties} && ($Options{propertiesmode} =~ /^All$/i) ) {
+    warn "Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n";
+  }
+  if ($Options{propertiesmode} =~ /^All$/i) {
+    if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
+      push @{$OptionsInfo{SpecifiedProperies}}, AminoAcids::GetAminoAcidPropertiesNames('Alphabetical');
+    }
+    else {
+      push @{$OptionsInfo{SpecifiedProperies}}, AminoAcids::GetAminoAcidPropertiesNames();
+    }
+  }
+  else {
+    if ($Options{properties}) {
+      if ($Options{propertiesmode} =~ /^Categories$/i) {
+	# Check category name...
+	if ($Options{properties} !~ /^(Basic|BasicPlus|BasicAndHydrophobicity|BasicAndHydrophobicityPlus)$/i) {
+	  die "Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic, BasicPlus, BasicAndHydrophobicity, and BasicAndHydrophobicityPlus\n";
+	}
+	# Set propertynames...
+	push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories($Options{properties});
+      }
+      else {
+	# Check property names..
+	my($Name, $PropertyName, @Names);
+	@Names = split /\,/, $Options{properties};
+	NAME: for $Name (@Names) {
+	  $PropertyName = RemoveLeadingAndTrailingWhiteSpaces($Name);
+	  if (AminoAcids::IsAminoAcidProperty($PropertyName)) {
+	    push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName;
+	  }
+	  else {
+	    warn "Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n";
+	  }
+	}
+	if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
+	  # ThreeLetterCode, OneLetterCode and AminoAcid are always listed first...
+	  # NaturalIsotopeData in the end...
+	  my($OneLetterCodePresent, $ThreeLetterCodePresent, $AminoAcidPresent,  @AlphabeticalProperties, %PropertiesMap);
+	  %PropertiesMap = ();
+	  @AlphabeticalProperties = ();
+	  $OneLetterCodePresent = 0; $ThreeLetterCodePresent = 0; $AminoAcidPresent = 0;
+	  NAME: for $Name (@{$OptionsInfo{SpecifiedProperies}}) {
+	    if ($Name =~ /^OneLetterCode$/i) {
+	      $OneLetterCodePresent = 1;
+	      next NAME;
+	    }
+	    if ($Name =~ /^ThreeLetterCode$/i) {
+	      $ThreeLetterCodePresent = 1;
+	      next NAME;
+	    }
+	    if ($Name =~ /^AminoAcid$/i) {
+	      $AminoAcidPresent = 1;
+	      next NAME;
+	    }
+	    $PropertiesMap{$Name} = $Name;
+	  }
+	  # Setup the alphabetical list...
+	  if ($ThreeLetterCodePresent) {
+	    push @AlphabeticalProperties, 'ThreeLetterCode';
+	  }
+	  if ($OneLetterCodePresent) {
+	    push @AlphabeticalProperties, 'OneLetterCode';
+	  }
+	  if ($AminoAcidPresent) {
+	    push @AlphabeticalProperties, 'AminoAcid';
+	  }
+	  for $Name (sort keys %PropertiesMap) {
+	    push @AlphabeticalProperties, $Name;
+	  }
+	  @{$OptionsInfo{SpecifiedProperies}} = ();
+	  push @{$OptionsInfo{SpecifiedProperies}}, @AlphabeticalProperties;
+	}
+      }
+    }
+    else {
+      # Set default value...
+      push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories('Basic');
+    }
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{outdelim} = "comma";
+  $Options{output} = "STDOUT";
+  $Options{outputstyle} = "AminoAcidBlock";
+  $Options{precision} = 4;
+  $Options{propertiesmode} = "Categories";
+  $Options{propertieslisting} = "ByGroup";
+  $Options{quote} = "yes";
+
+  if (!GetOptions(\%Options, "help|h", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "properties|p=s", "propertieslisting=s", "propertiesmode=s", "quote|q=s", "root|r=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{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{output} !~ /^(STDOUT|File)$/i) {
+    die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n";
+  }
+  if ($Options{outputstyle} !~ /^(AminoAcidBlock|AminoAcidRows)$/i) {
+    die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: AminoAcidBlock or AminoAcidRows\n";
+  }
+  if (!IsPositiveInteger($Options{precision})) {
+    die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{propertiesmode} !~ /^(Categories|Names|All)$/i) {
+    die "Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n";
+  }
+  if ($Options{propertieslisting} !~ /^(ByGroup|Alphabetical)$/i) {
+    die "Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n";
+  }
+  if ($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
+
+InfoAminoAcids.pl - List properties of amino acids
+
+=head1 SYNOPSIS
+
+InfoAminoAcids.pl AminoAcidIDs...
+
+InfoAminoAcids.pl [B<-h, --help>] [B<--outdelim> comma | tab | semicolon]
+[B<--output> STDOUT | File] [B<--outputstyle> AminoAcidBlock | AminoAcidRows]
+[B<-o, --overwrite>] [B<--precision> number] [B<--propertiesmode> Categories | Names | All]
+[B<-p, --properties> CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]]
+[B<--propertieslinting> ByGroup | Alphabetical] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
+[B<-w, --workingdir> dirname] AminoAcidIDs...
+
+=head1 DESCRIPTION
+
+List amino acid properties. Amino acids identification supports these three types of IDs: one letter
+code, three letter code or name. Amino acid properties data, in addition to basic information about
+amino acids - one and three letter codes, name, DNA and RNA codons, molecular weight - include
+variety of other properties: polarity, acidity, hydrophobicity, and so on.
+
+=head1 PARAMETERS
+
+=over 4
+
+=item B<AminoAcidIDs> I<ThreeLetterCode [OneLetterCode AminoAcidName...]>
+
+I<AminoAcidIDs> is a space delimited list of values to identify amino acids.
+
+Input value format is: I<ThreeLetterCode [OneLetterCode AminoAcidName...]>. Default: I<Ala>.
+Examples:
+
+    Ala
+    Glu A
+    Alanine Glu Y "Aspartic acid"
+
+=back
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<--outdelim> I<comma | tab | semicolon>
+
+Output text file delimiter. Possible values: I<comma, tab, or semicolon>
+Default value: I<comma>.
+
+=item B<--output> I<STDOUT | File>
+
+List information at STDOUT or write it to a file. Possible values: I<STDOUT or File>. Default:
+I<STDOUT>. B<-r, --root> option is used to generate output file name.
+
+=item B<--outputstyle> I<AminoAcidBlock | AminoAcidRows>
+
+Specify how to list amino acid information: add a new line for each property and present it as a block
+for each amino acid; or include all properties in one line and show it as a single line.
+
+Possible values: I<AminoAcidBlock | AminoAcidRows>. Default: I<AminoAcidBlock>
+
+An example for I<AminoAcidBlock> output style:
+
+    ThreeLetterCode: Ala
+    OneLetterCode: A
+    AminoAcid: Alanine
+    MolecularWeight: 89.0941
+    ... ...
+    ... ...
+    ... ...
+
+    ThreeLetterCode: Glu
+    OneLetterCode: E
+    AminoAcid: Glutamic acid
+    MolecularWeight: 147.1308
+    ... ...
+    ... ...
+    ... ...
+
+An example for I<AminoAcidRows> output style:
+
+    ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
+    Ala,A,Alanine,89.0941..
+    Glu,E,Glutamic acid,147.1308..
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<--precision> I<number>
+
+Precision for listing numerical values. Default: up to I<4> decimal places.
+Valid values: positive integers.
+
+=item B<--propertiesmode> I<Categories | Names | All>
+
+Specify how property names are specified: use category names; explicit list of property names; or
+use all available properties. Possible values: I<Categories, Names, or All>. Default: I<Categories>.
+
+This option is used in conjunction with B<-p, --properties> option to specify properties of
+interest.
+
+=item B<-p, --properties> I<CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]>
+
+This option is B<--propertiesmode> specific. In general, it's a list of comma separated category or
+property names.
+
+Specify which amino acid properties information to list for the amino acid IDs specified using command:
+line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma
+separated list of amino acid property names.
+
+Possible values: I<Basic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]>.
+Default: I<Basic>.
+
+I<Basic> includes: I<ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4>
+
+I<BasicPlus> includes: I<ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), LinearStructure, LinearStructureAtpH7.4>
+
+I<BasicAndHydrophobicity> includes: I<ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers>
+
+I<BasicAndHydrophobicityPlus> includes: I<(ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers>
+
+Here is a complete list of available properties: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume, %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition, AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility, BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt, BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers, ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide, RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4
+
+=item B<--propertieslisting> I<ByGroup | Alphabetical>
+
+Specify how to list properties for amino acids: group by category or an alphabetical by
+property names. Possible values: I<ByGroup or Alphabetical>. Default: I<ByGroup>.
+
+=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>. File name is only
+used during I<File> value of B<-o, --output> option.
+
+Default file name: AminoAcidInfo<mode>.<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 list basic properties information for amino acid Ala, type:
+
+    % InfoAminoAcids.pl
+
+To list all available properties information for amino acid Ala, type:
+
+    % InfoAminoAcids.pl --propertiesmode all
+
+To list basic properties information for amino acids Ala, Arg, and Asp type:
+
+    % InfoAminoAcids.pl Ala Arg Asp
+    % InfoAminoAcids.pl A Arg "Aspartic acid"
+
+To list all available properties information for amino acids Ala, Arg, and Asp type:
+
+    % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp
+
+To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:
+
+    % InfoAminoAcids.pl --propertiesmode Categories
+      --properties BasicAndHydrophobicity Ala Arg Asp
+
+To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino
+acids Ala, Arg, and Asp type:
+
+    % InfoAminoAcids.pl --propertiesmode Names
+      --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight
+      Ala Arg Asp
+
+To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
+in rows insetad of amino acid blocks with quotes around the values, type:
+
+    % InfoAminoAcids.pl --propertiesmode Categories
+      --properties BasicAndHydrophobicity --propertieslisting alphabetical
+      --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp
+
+To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp
+in rows insetad of amino acid blocks with quotes around the values and write them into a file
+AminoAcidProperties.csv, type:
+
+    % InfoAminoAcids.pl --propertiesmode Categories
+      --properties BasicAndHydrophobicity --propertieslisting alphabetical
+      --outdelim comma --outputstyle AminoAcidRows --quote yes
+      --output File -r AminoAcidProperties -o Ala Arg Asp
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+InfoNucleicAcids.pl InfoPeriodicTableElements.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