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author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/NucleicAcids.pm	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,475 @@
+package NucleicAcids;
+#
+# $RCSfile: NucleicAcids.pm,v $
+# $Date: 2015/02/28 20:47:18 $
+# $Revision: 1.25 $
+#
+# 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 Carp;
+use Text::ParseWords;
+use TextUtil;
+use FileUtil;
+
+use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
+
+@ISA = qw(Exporter);
+@EXPORT = qw();
+@EXPORT_OK = qw(GetNucleicAcids GetNucleicAcidsByType GetNucleicAcidPropertiesData GetNucleicAcidPropertiesNames IsNucleicAcid IsNucleicAcidProperty IsNucleicAcidType);
+
+%EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
+
+#
+# Load nucleic acids data...
+#
+my(%NucleicAcidDataMap, %NucleicAcidCodeMap, %NucleicAcidOtherCodeMap, %NucleicAcidNameMap, @NucleicAcidCodes, @NucleicAcidPropertyNames, %NucleicAcidPropertyNamesMap, %NucleicAcidTypesMap);
+_LoadNucleicAcidsData();
+
+#
+# Get a list of all known nucleic acids as one of these values:
+# code or nucleic acid name...
+#
+sub GetNucleicAcids {
+  my($NameType, $Code, $Name, @NucleicAcidNames);
+
+  $NameType = 'Code';
+  if (@_ >= 1) {
+    ($NameType) = @_;
+  }
+
+  # Collect names...
+  @NucleicAcidNames = ();
+  for $Code (@NucleicAcidCodes) {
+    NAME : {
+      if ($NameType =~ /^Name$/i) {$Name = $NucleicAcidDataMap{$Code}{Name}; last NAME; }
+      $Name = $Code;
+    }
+    push @NucleicAcidNames, $Name;
+  }
+
+  return (wantarray ? @NucleicAcidNames : \@NucleicAcidNames);
+}
+
+#
+# Get a list of all known nucleic acids by one of these specified types:
+# Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside
+#
+sub GetNucleicAcidsByType {
+  my($NameType, $Type, $Code, $Name, @NucleicAcidNames);
+
+  $Type = 'Nucleoside';
+  $NameType = 'Code';
+  if (@_ == 2) {
+    ($Type, $NameType) = @_;
+  }
+  elsif (@_ == 1) {
+    ($Type) = @_;
+  }
+
+  # Collect names...
+  @NucleicAcidNames = ();
+  CODE: for $Code (@NucleicAcidCodes) {
+    if ($NucleicAcidDataMap{$Code}{Type} !~ /^$Type$/i ) {
+      next CODE;
+    }
+    NAME : {
+      if ($NameType =~ /^Name$/i) {$Name = $NucleicAcidDataMap{$Code}{Name}; last NAME; }
+      $Name = $Code;
+    }
+    push @NucleicAcidNames, $Name;
+  }
+
+  return (wantarray ? @NucleicAcidNames : \@NucleicAcidNames);
+}
+
+#
+# Get all available properties data for an nucleic acid using any of these symbols:
+# code, other code or name.
+#
+# A reference to a hash array is returned with keys and values representing property
+# name and its values respectively.
+#
+sub GetNucleicAcidPropertiesData {
+  my($NucleicAcidID) = @_;
+  my($Code);
+
+  if ($Code = _ValidateNucleicAcidID($NucleicAcidID)) {
+    return \%{$NucleicAcidDataMap{$Code}};
+  }
+  else {
+    return undef;
+  }
+}
+
+#
+# Get names of all available nucleic acid properties. A reference to  an array containing
+# names of all available properties is returned.
+#
+sub GetNucleicAcidPropertiesNames {
+  my($Mode);
+  my($PropertyName, @PropertyNames);
+
+  $Mode = 'ByGroup';
+  if (@_ == 1) {
+    ($Mode) = @_;
+  }
+
+  @PropertyNames = ();
+  if ($Mode =~ /^Alphabetical$/i) {
+    my($PropertyName);
+    # Code, OtherCodes and Name are always listed first...
+    push @PropertyNames, qw(Code OtherCodes Name);
+    for $PropertyName (sort keys %NucleicAcidPropertyNamesMap) {
+      if ($PropertyName !~ /^(Code|OtherCodes|Name)$/) {
+	push @PropertyNames, $PropertyName;
+      }
+    }
+  }
+  else {
+    push @PropertyNames, @NucleicAcidPropertyNames;
+  }
+  return (wantarray ? @PropertyNames : \@PropertyNames);
+}
+
+#
+# Is it a known nucleic acid? Input is either a code or a name
+#
+sub IsNucleicAcid {
+  my($NucleicAcidID) = @_;
+  my($Status);
+
+  $Status = (_ValidateNucleicAcidID($NucleicAcidID)) ? 1 : 0;
+
+  return $Status;
+}
+
+#
+# Is it an available nucleic acid property?
+#
+sub IsNucleicAcidProperty {
+  my($PropertyName) = @_;
+  my($Status);
+
+  $Status = (exists($NucleicAcidPropertyNamesMap{$PropertyName})) ? 1 : 0;
+
+  return $Status;
+}
+
+#
+# Is it an available nucleic acid type?
+#
+sub IsNucleicAcidType {
+  my($Type) = @_;
+  my($Status);
+
+  $Status = (exists($NucleicAcidTypesMap{lc($Type)})) ? 1 : 0;
+
+  return $Status;
+}
+
+#
+# Implents GetNucleicAcid<PropertyName> for a valid proprty name.
+#
+sub AUTOLOAD {
+  my($NucleicAcidID) = @_;
+  my($FunctionName, $PropertyName, $PropertyValue, $Code);
+
+  $PropertyValue = undef;
+
+  use vars qw($AUTOLOAD);
+  $FunctionName = $AUTOLOAD;
+  $FunctionName =~ s/.*:://;
+
+  # Only Get<PropertyName> functions are supported...
+  if ($FunctionName !~ /^Get/) {
+    croak "Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Only Get<PropertyName> functions are implemented...";
+  }
+
+  $PropertyName = $FunctionName;
+  $PropertyName =~  s/^GetNucleicAcid//;
+  if (!exists $NucleicAcidPropertyNamesMap{$PropertyName}) {
+    croak "Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Unknown nucleic acid property name, $PropertyName, specified...";
+  }
+
+  if (!($Code = _ValidateNucleicAcidID($NucleicAcidID))) {
+    return undef;
+  }
+  $PropertyValue = $NucleicAcidDataMap{$Code}{$PropertyName};
+  return $PropertyValue;
+}
+
+#
+# Load NucleicAcidsData.csv files from <MayaChemTools>/lib directory...
+#
+sub _LoadNucleicAcidsData {
+  my($NucleicAcidsDataFile, $MayaChemToolsLibDir);
+
+  $MayaChemToolsLibDir = GetMayaChemToolsLibDirName();
+
+  $NucleicAcidsDataFile =  "$MayaChemToolsLibDir" . "/data/NucleicAcidsData.csv";
+
+  if (! -e "$NucleicAcidsDataFile") {
+    croak "Error: MayaChemTools package file, $NucleicAcidsDataFile, is missing: Possible installation problems...";
+  }
+
+  _LoadData($NucleicAcidsDataFile);
+}
+
+#
+# Load NucleicAcidsData.csv file from <MayaChemTools>/lib directory...
+#
+sub _LoadData {
+  my($NucleicAcidsDataFile) = @_;
+
+  %NucleicAcidDataMap = ();
+  @NucleicAcidCodes = ();
+  @NucleicAcidPropertyNames = ();
+  %NucleicAcidPropertyNamesMap = ();
+  %NucleicAcidCodeMap = ();
+  %NucleicAcidOtherCodeMap = ();
+  %NucleicAcidNameMap = ();
+  %NucleicAcidTypesMap = ();
+
+  # Load property data for all nucleic acids...
+  #
+  # File Format:
+  # "Code","OtherCodes","BasePair","Name","Type","ChemicalFormula","ChemicalFormulaAtpH7.5","MolecularWeight","ExactMass","ElementalComposition"
+  #
+  my($Code, $OtherCodes, $NucleicAcidName, $Line, $NumOfCols, $InDelim, $Index, $Name, $Value, $Units, @LineWords, @ColLabels);
+
+  $InDelim = "\,";
+  open NUCLEICACIDSDATAFILE, "$NucleicAcidsDataFile" or croak "Couldn't open $NucleicAcidsDataFile: $! ...";
+
+  # Skip lines up to column labels...
+  LINE: while ($Line = GetTextLine(\*NUCLEICACIDSDATAFILE)) {
+    if ($Line !~ /^#/) {
+      last LINE;
+    }
+  }
+  @ColLabels= quotewords($InDelim, 0, $Line);
+  $NumOfCols = @ColLabels;
+
+  # Extract property names from column labels...
+  @NucleicAcidPropertyNames = ();
+  for $Index (0 .. $#ColLabels) {
+    $Name = $ColLabels[$Index];
+    push @NucleicAcidPropertyNames, $Name;
+
+    # Store property names...
+    $NucleicAcidPropertyNamesMap{$Name} = $Name;
+  }
+
+  # Process nucleic acid data...
+  LINE: while ($Line = GetTextLine(\*NUCLEICACIDSDATAFILE)) {
+    if ($Line =~ /^#/) {
+      next LINE;
+    }
+    @LineWords = ();
+    @LineWords = quotewords($InDelim, 0, $Line);
+    if (@LineWords != $NumOfCols) {
+      croak "Error: The number of data fields, @LineWords, in $NucleicAcidsDataFile must be $NumOfCols.\nLine: $Line...";
+    }
+    $Code = $LineWords[0]; $OtherCodes = $LineWords[1]; $NucleicAcidName = $LineWords[3];
+    if (exists $NucleicAcidDataMap{$Code}) {
+      carp "Warning: Ignoring data for nucleic acid $Code: It has already been loaded.\nLine: $Line....";
+      next LINE;
+    }
+
+    # Store all the values...
+    push @NucleicAcidCodes, $Code;
+    %{$NucleicAcidDataMap{$Code}} = ();
+    for $Index (0 .. $#LineWords) {
+      $Name = $NucleicAcidPropertyNames[$Index];
+      $Value = $LineWords[$Index];
+      $NucleicAcidDataMap{$Code}{$Name} = $Value;
+    }
+  }
+  close NUCLEICACIDSDATAFILE;
+
+  # Setup one letter and nucleic acid name maps...
+  _SetupNucleicAcidIDMap();
+}
+
+#
+# Setup lowercase other codes and name maps pointing
+# to code as show in data file.
+#
+sub _SetupNucleicAcidIDMap {
+  my($Code, @OtherCodes, $OtherCode, $NucleicAcidName, $NucleicAcidType);
+
+  %NucleicAcidCodeMap = ();
+  %NucleicAcidOtherCodeMap = ();
+  %NucleicAcidNameMap = ();
+  %NucleicAcidTypesMap = ();
+
+  for $Code (keys %NucleicAcidDataMap) {
+    $NucleicAcidCodeMap{lc($Code)} = $Code;
+
+    $NucleicAcidName = $NucleicAcidDataMap{$Code}{Name};
+    $NucleicAcidNameMap{lc($NucleicAcidName)} = $Code;
+
+    $NucleicAcidType = $NucleicAcidDataMap{$Code}{Type};
+    if (! exists $NucleicAcidTypesMap{$NucleicAcidType}) {
+      $NucleicAcidTypesMap{lc($NucleicAcidType)} = $NucleicAcidType;
+    }
+
+    @OtherCodes = split /\,/, $NucleicAcidDataMap{$Code}{OtherCodes};
+    OTHERCODE: for $OtherCode (@OtherCodes) {
+      if (!$OtherCode) {
+	next OTHERCODE;
+      }
+      $OtherCode = RemoveLeadingAndTrailingWhiteSpaces($OtherCode);
+      $NucleicAcidOtherCodeMap{lc($OtherCode)} = $Code;
+    }
+  }
+}
+
+# Validate Nucleic acid ID...
+sub _ValidateNucleicAcidID {
+  my($NucleicAcidID) = @_;
+  my($Code) = undef;
+
+  if (exists $NucleicAcidCodeMap{lc($NucleicAcidID)}) {
+    $Code = $NucleicAcidCodeMap{lc($NucleicAcidID)};
+  }
+  elsif (exists $NucleicAcidOtherCodeMap{lc($NucleicAcidID)}) {
+    $Code = $NucleicAcidOtherCodeMap{lc($NucleicAcidID)};
+  }
+  elsif (exists $NucleicAcidNameMap{lc($NucleicAcidID)}) {
+    $Code = $NucleicAcidNameMap{lc($NucleicAcidID)};
+  }
+  return $Code;
+}
+
+
+1;
+
+__END__
+
+=head1 NAME
+
+NucleicAcids
+
+=head1 SYNOPSIS
+
+use NucleicAcids;
+
+use NucleicAcids qw(:all);
+
+=head1 DESCRIPTION
+
+B<NucleicAcids> module the provides the following functions:
+
+GetNucleicAcidPropertiesData, GetNucleicAcidPropertiesNames,
+GetNucleicAcids, GetNucleicAcidsByType, IsNucleicAcid, IsNucleicAcidProperty,
+IsNucleicAcidType
+
+=head1 Functions
+
+=over 4
+
+=item B<GetNucleicAcids>
+
+    (@Names) = GetNucleicAcids([$NameType]);
+    $NamesRef = GetNucleicAcids([$NameType]);
+
+Returns an array or a reference to an array containing names of nucleic acids
+as a code or nucleic acid name controlled by optional parameter I<NameType>. By
+default, nucleic acids names are returned as the code. Possible values for
+I<NameType>: I<Code or Name>.
+
+=item B<GetNucleicAcidsByType>
+
+    (@Names) = GetNucleicAcidsByType([$Type, $NameType]);
+    $NamesRef = GetNucleicAcidsByType([$Type, $NameType]);
+
+Returns an array or a reference to an array containing names of nucleic acids
+specified by parameter I<Type> as a code or name controlled by optional
+parameter I<NameType>. Default values for I<Type>: I<Nucleoside>. Default value for
+I<NameType>: I<Code>. Possible values for I<Type>: I<Nucleobase, Nucleoside, Deoxynucleoside,
+Nucleotide, Deoxynucleotide>. Possible values for I<NameType>: I<Code or Name>.
+
+=item B<GetNucleicAcidPropertiesData>
+
+    $DataHashRef = GetNucleicAcidPropertiesData($NucleicAcidID);
+
+Returns a reference to hash containing property names and values for a specified
+I<NucleicAcidID>.
+
+=item B<GetNucleicAcidPropertyName>
+
+    $Value = GetNucleicAcid<PropertyName>($NucleicAcidID);
+
+Returns nucleic acid property value for a specified I<NucleicAcidID>. This function is
+implemented on-the-fly using Perl's AUTOLOAD functionality.
+
+=item B<GetNucleicAcidPropertiesNames>
+
+    @Names = GetNucleicAcidPropertiesNames([$Mode]);
+    $NamesRef = GetNucleicAcidPropertiesNames([$Mode]);
+
+Returns an array or a reference to an array containing names of properties for
+nucleic acids. Order of nucleic acids properties is controlled by optional parameter
+I<Mode>. Possible values for I<Mode>: I<Alphabetical or ByGroup>; Default: I<ByGroup>.
+
+=item B<IsNucleicAcid>
+
+    $Status = IsNucleicAcid($NucleicAcidID);
+
+Returns 1 or 0 based on whether it's a known nucleic acid ID.
+
+=item B<IsNucleicAcidProperty>
+
+    $Status = IsNucleicAcid($PropertyName);
+
+Returns 1 or 0 based on whether it's a known nucleic acid property name.
+
+=item B<IsNucleicAcidType>
+
+    $Status = IsNucleicAcidType();
+
+Returns 1 or 0 based on whether it's a known nucleic acid type.
+
+=back
+
+=head1 AUTHOR
+
+Manish Sud <msud@san.rr.com>
+
+=head1 SEE ALSO
+
+AminoAcids.pm, PeriodicTable.pm
+
+=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