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1 package NucleicAcids;
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2 #
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3 # $RCSfile: NucleicAcids.pm,v $
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4 # $Date: 2015/02/28 20:47:18 $
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5 # $Revision: 1.25 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use Carp;
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31 use Text::ParseWords;
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32 use TextUtil;
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33 use FileUtil;
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34
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35 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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36
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37 @ISA = qw(Exporter);
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38 @EXPORT = qw();
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39 @EXPORT_OK = qw(GetNucleicAcids GetNucleicAcidsByType GetNucleicAcidPropertiesData GetNucleicAcidPropertiesNames IsNucleicAcid IsNucleicAcidProperty IsNucleicAcidType);
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40
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41 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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42
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43 #
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44 # Load nucleic acids data...
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45 #
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46 my(%NucleicAcidDataMap, %NucleicAcidCodeMap, %NucleicAcidOtherCodeMap, %NucleicAcidNameMap, @NucleicAcidCodes, @NucleicAcidPropertyNames, %NucleicAcidPropertyNamesMap, %NucleicAcidTypesMap);
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47 _LoadNucleicAcidsData();
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48
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49 #
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50 # Get a list of all known nucleic acids as one of these values:
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51 # code or nucleic acid name...
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52 #
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53 sub GetNucleicAcids {
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54 my($NameType, $Code, $Name, @NucleicAcidNames);
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55
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56 $NameType = 'Code';
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57 if (@_ >= 1) {
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58 ($NameType) = @_;
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59 }
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60
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61 # Collect names...
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62 @NucleicAcidNames = ();
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63 for $Code (@NucleicAcidCodes) {
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64 NAME : {
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65 if ($NameType =~ /^Name$/i) {$Name = $NucleicAcidDataMap{$Code}{Name}; last NAME; }
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66 $Name = $Code;
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67 }
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68 push @NucleicAcidNames, $Name;
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69 }
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70
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71 return (wantarray ? @NucleicAcidNames : \@NucleicAcidNames);
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72 }
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73
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74 #
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75 # Get a list of all known nucleic acids by one of these specified types:
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76 # Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside
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77 #
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78 sub GetNucleicAcidsByType {
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79 my($NameType, $Type, $Code, $Name, @NucleicAcidNames);
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80
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81 $Type = 'Nucleoside';
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82 $NameType = 'Code';
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83 if (@_ == 2) {
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84 ($Type, $NameType) = @_;
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85 }
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86 elsif (@_ == 1) {
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87 ($Type) = @_;
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88 }
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89
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90 # Collect names...
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91 @NucleicAcidNames = ();
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92 CODE: for $Code (@NucleicAcidCodes) {
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93 if ($NucleicAcidDataMap{$Code}{Type} !~ /^$Type$/i ) {
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94 next CODE;
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95 }
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96 NAME : {
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97 if ($NameType =~ /^Name$/i) {$Name = $NucleicAcidDataMap{$Code}{Name}; last NAME; }
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98 $Name = $Code;
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99 }
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100 push @NucleicAcidNames, $Name;
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101 }
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102
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103 return (wantarray ? @NucleicAcidNames : \@NucleicAcidNames);
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104 }
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105
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106 #
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107 # Get all available properties data for an nucleic acid using any of these symbols:
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108 # code, other code or name.
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109 #
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110 # A reference to a hash array is returned with keys and values representing property
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111 # name and its values respectively.
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112 #
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113 sub GetNucleicAcidPropertiesData {
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114 my($NucleicAcidID) = @_;
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115 my($Code);
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116
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117 if ($Code = _ValidateNucleicAcidID($NucleicAcidID)) {
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118 return \%{$NucleicAcidDataMap{$Code}};
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119 }
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120 else {
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121 return undef;
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122 }
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123 }
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124
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125 #
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126 # Get names of all available nucleic acid properties. A reference to an array containing
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127 # names of all available properties is returned.
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128 #
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129 sub GetNucleicAcidPropertiesNames {
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130 my($Mode);
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131 my($PropertyName, @PropertyNames);
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132
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133 $Mode = 'ByGroup';
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134 if (@_ == 1) {
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135 ($Mode) = @_;
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136 }
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137
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138 @PropertyNames = ();
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139 if ($Mode =~ /^Alphabetical$/i) {
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140 my($PropertyName);
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141 # Code, OtherCodes and Name are always listed first...
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142 push @PropertyNames, qw(Code OtherCodes Name);
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143 for $PropertyName (sort keys %NucleicAcidPropertyNamesMap) {
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144 if ($PropertyName !~ /^(Code|OtherCodes|Name)$/) {
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145 push @PropertyNames, $PropertyName;
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146 }
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147 }
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148 }
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149 else {
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150 push @PropertyNames, @NucleicAcidPropertyNames;
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151 }
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152 return (wantarray ? @PropertyNames : \@PropertyNames);
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153 }
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154
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155 #
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156 # Is it a known nucleic acid? Input is either a code or a name
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157 #
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158 sub IsNucleicAcid {
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159 my($NucleicAcidID) = @_;
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160 my($Status);
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161
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162 $Status = (_ValidateNucleicAcidID($NucleicAcidID)) ? 1 : 0;
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163
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164 return $Status;
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165 }
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166
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167 #
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168 # Is it an available nucleic acid property?
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169 #
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170 sub IsNucleicAcidProperty {
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171 my($PropertyName) = @_;
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172 my($Status);
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173
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174 $Status = (exists($NucleicAcidPropertyNamesMap{$PropertyName})) ? 1 : 0;
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175
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176 return $Status;
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177 }
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178
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179 #
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180 # Is it an available nucleic acid type?
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181 #
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182 sub IsNucleicAcidType {
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183 my($Type) = @_;
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184 my($Status);
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185
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186 $Status = (exists($NucleicAcidTypesMap{lc($Type)})) ? 1 : 0;
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187
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188 return $Status;
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189 }
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190
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191 #
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192 # Implents GetNucleicAcid<PropertyName> for a valid proprty name.
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193 #
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194 sub AUTOLOAD {
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195 my($NucleicAcidID) = @_;
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196 my($FunctionName, $PropertyName, $PropertyValue, $Code);
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197
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198 $PropertyValue = undef;
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199
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200 use vars qw($AUTOLOAD);
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201 $FunctionName = $AUTOLOAD;
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202 $FunctionName =~ s/.*:://;
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203
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204 # Only Get<PropertyName> functions are supported...
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205 if ($FunctionName !~ /^Get/) {
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206 croak "Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Only Get<PropertyName> functions are implemented...";
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207 }
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208
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209 $PropertyName = $FunctionName;
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210 $PropertyName =~ s/^GetNucleicAcid//;
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211 if (!exists $NucleicAcidPropertyNamesMap{$PropertyName}) {
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212 croak "Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Unknown nucleic acid property name, $PropertyName, specified...";
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213 }
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214
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215 if (!($Code = _ValidateNucleicAcidID($NucleicAcidID))) {
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216 return undef;
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217 }
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218 $PropertyValue = $NucleicAcidDataMap{$Code}{$PropertyName};
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219 return $PropertyValue;
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220 }
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221
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222 #
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223 # Load NucleicAcidsData.csv files from <MayaChemTools>/lib directory...
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224 #
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225 sub _LoadNucleicAcidsData {
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226 my($NucleicAcidsDataFile, $MayaChemToolsLibDir);
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227
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228 $MayaChemToolsLibDir = GetMayaChemToolsLibDirName();
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229
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230 $NucleicAcidsDataFile = "$MayaChemToolsLibDir" . "/data/NucleicAcidsData.csv";
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231
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232 if (! -e "$NucleicAcidsDataFile") {
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233 croak "Error: MayaChemTools package file, $NucleicAcidsDataFile, is missing: Possible installation problems...";
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234 }
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235
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236 _LoadData($NucleicAcidsDataFile);
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237 }
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238
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239 #
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240 # Load NucleicAcidsData.csv file from <MayaChemTools>/lib directory...
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241 #
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242 sub _LoadData {
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243 my($NucleicAcidsDataFile) = @_;
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244
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245 %NucleicAcidDataMap = ();
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246 @NucleicAcidCodes = ();
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247 @NucleicAcidPropertyNames = ();
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248 %NucleicAcidPropertyNamesMap = ();
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249 %NucleicAcidCodeMap = ();
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250 %NucleicAcidOtherCodeMap = ();
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251 %NucleicAcidNameMap = ();
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252 %NucleicAcidTypesMap = ();
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253
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254 # Load property data for all nucleic acids...
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255 #
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256 # File Format:
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257 # "Code","OtherCodes","BasePair","Name","Type","ChemicalFormula","ChemicalFormulaAtpH7.5","MolecularWeight","ExactMass","ElementalComposition"
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258 #
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259 my($Code, $OtherCodes, $NucleicAcidName, $Line, $NumOfCols, $InDelim, $Index, $Name, $Value, $Units, @LineWords, @ColLabels);
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260
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261 $InDelim = "\,";
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262 open NUCLEICACIDSDATAFILE, "$NucleicAcidsDataFile" or croak "Couldn't open $NucleicAcidsDataFile: $! ...";
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263
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264 # Skip lines up to column labels...
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265 LINE: while ($Line = GetTextLine(\*NUCLEICACIDSDATAFILE)) {
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266 if ($Line !~ /^#/) {
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267 last LINE;
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268 }
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269 }
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270 @ColLabels= quotewords($InDelim, 0, $Line);
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271 $NumOfCols = @ColLabels;
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272
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273 # Extract property names from column labels...
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274 @NucleicAcidPropertyNames = ();
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275 for $Index (0 .. $#ColLabels) {
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276 $Name = $ColLabels[$Index];
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277 push @NucleicAcidPropertyNames, $Name;
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278
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279 # Store property names...
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280 $NucleicAcidPropertyNamesMap{$Name} = $Name;
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281 }
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282
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283 # Process nucleic acid data...
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284 LINE: while ($Line = GetTextLine(\*NUCLEICACIDSDATAFILE)) {
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285 if ($Line =~ /^#/) {
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286 next LINE;
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287 }
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288 @LineWords = ();
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289 @LineWords = quotewords($InDelim, 0, $Line);
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290 if (@LineWords != $NumOfCols) {
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291 croak "Error: The number of data fields, @LineWords, in $NucleicAcidsDataFile must be $NumOfCols.\nLine: $Line...";
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292 }
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293 $Code = $LineWords[0]; $OtherCodes = $LineWords[1]; $NucleicAcidName = $LineWords[3];
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294 if (exists $NucleicAcidDataMap{$Code}) {
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295 carp "Warning: Ignoring data for nucleic acid $Code: It has already been loaded.\nLine: $Line....";
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296 next LINE;
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297 }
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298
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299 # Store all the values...
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300 push @NucleicAcidCodes, $Code;
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301 %{$NucleicAcidDataMap{$Code}} = ();
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302 for $Index (0 .. $#LineWords) {
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303 $Name = $NucleicAcidPropertyNames[$Index];
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304 $Value = $LineWords[$Index];
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305 $NucleicAcidDataMap{$Code}{$Name} = $Value;
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306 }
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307 }
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308 close NUCLEICACIDSDATAFILE;
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309
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310 # Setup one letter and nucleic acid name maps...
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311 _SetupNucleicAcidIDMap();
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312 }
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313
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314 #
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315 # Setup lowercase other codes and name maps pointing
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316 # to code as show in data file.
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317 #
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318 sub _SetupNucleicAcidIDMap {
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319 my($Code, @OtherCodes, $OtherCode, $NucleicAcidName, $NucleicAcidType);
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320
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321 %NucleicAcidCodeMap = ();
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322 %NucleicAcidOtherCodeMap = ();
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323 %NucleicAcidNameMap = ();
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324 %NucleicAcidTypesMap = ();
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325
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326 for $Code (keys %NucleicAcidDataMap) {
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327 $NucleicAcidCodeMap{lc($Code)} = $Code;
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328
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329 $NucleicAcidName = $NucleicAcidDataMap{$Code}{Name};
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330 $NucleicAcidNameMap{lc($NucleicAcidName)} = $Code;
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331
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332 $NucleicAcidType = $NucleicAcidDataMap{$Code}{Type};
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333 if (! exists $NucleicAcidTypesMap{$NucleicAcidType}) {
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334 $NucleicAcidTypesMap{lc($NucleicAcidType)} = $NucleicAcidType;
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335 }
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336
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337 @OtherCodes = split /\,/, $NucleicAcidDataMap{$Code}{OtherCodes};
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338 OTHERCODE: for $OtherCode (@OtherCodes) {
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339 if (!$OtherCode) {
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340 next OTHERCODE;
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341 }
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342 $OtherCode = RemoveLeadingAndTrailingWhiteSpaces($OtherCode);
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343 $NucleicAcidOtherCodeMap{lc($OtherCode)} = $Code;
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344 }
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345 }
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346 }
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347
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348 # Validate Nucleic acid ID...
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349 sub _ValidateNucleicAcidID {
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350 my($NucleicAcidID) = @_;
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351 my($Code) = undef;
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352
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353 if (exists $NucleicAcidCodeMap{lc($NucleicAcidID)}) {
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354 $Code = $NucleicAcidCodeMap{lc($NucleicAcidID)};
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355 }
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356 elsif (exists $NucleicAcidOtherCodeMap{lc($NucleicAcidID)}) {
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357 $Code = $NucleicAcidOtherCodeMap{lc($NucleicAcidID)};
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358 }
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359 elsif (exists $NucleicAcidNameMap{lc($NucleicAcidID)}) {
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360 $Code = $NucleicAcidNameMap{lc($NucleicAcidID)};
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361 }
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362 return $Code;
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363 }
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364
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365
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366 1;
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367
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368 __END__
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369
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370 =head1 NAME
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371
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372 NucleicAcids
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373
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374 =head1 SYNOPSIS
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375
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376 use NucleicAcids;
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377
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378 use NucleicAcids qw(:all);
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379
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380 =head1 DESCRIPTION
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381
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382 B<NucleicAcids> module the provides the following functions:
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383
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384 GetNucleicAcidPropertiesData, GetNucleicAcidPropertiesNames,
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385 GetNucleicAcids, GetNucleicAcidsByType, IsNucleicAcid, IsNucleicAcidProperty,
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386 IsNucleicAcidType
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387
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388 =head1 Functions
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389
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390 =over 4
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391
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392 =item B<GetNucleicAcids>
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393
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394 (@Names) = GetNucleicAcids([$NameType]);
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395 $NamesRef = GetNucleicAcids([$NameType]);
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396
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397 Returns an array or a reference to an array containing names of nucleic acids
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398 as a code or nucleic acid name controlled by optional parameter I<NameType>. By
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399 default, nucleic acids names are returned as the code. Possible values for
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400 I<NameType>: I<Code or Name>.
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401
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402 =item B<GetNucleicAcidsByType>
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403
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404 (@Names) = GetNucleicAcidsByType([$Type, $NameType]);
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405 $NamesRef = GetNucleicAcidsByType([$Type, $NameType]);
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406
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407 Returns an array or a reference to an array containing names of nucleic acids
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408 specified by parameter I<Type> as a code or name controlled by optional
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409 parameter I<NameType>. Default values for I<Type>: I<Nucleoside>. Default value for
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410 I<NameType>: I<Code>. Possible values for I<Type>: I<Nucleobase, Nucleoside, Deoxynucleoside,
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411 Nucleotide, Deoxynucleotide>. Possible values for I<NameType>: I<Code or Name>.
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412
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413 =item B<GetNucleicAcidPropertiesData>
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414
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415 $DataHashRef = GetNucleicAcidPropertiesData($NucleicAcidID);
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416
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417 Returns a reference to hash containing property names and values for a specified
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418 I<NucleicAcidID>.
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419
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420 =item B<GetNucleicAcidPropertyName>
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421
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422 $Value = GetNucleicAcid<PropertyName>($NucleicAcidID);
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423
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424 Returns nucleic acid property value for a specified I<NucleicAcidID>. This function is
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425 implemented on-the-fly using Perl's AUTOLOAD functionality.
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426
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427 =item B<GetNucleicAcidPropertiesNames>
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428
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429 @Names = GetNucleicAcidPropertiesNames([$Mode]);
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430 $NamesRef = GetNucleicAcidPropertiesNames([$Mode]);
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431
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432 Returns an array or a reference to an array containing names of properties for
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433 nucleic acids. Order of nucleic acids properties is controlled by optional parameter
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434 I<Mode>. Possible values for I<Mode>: I<Alphabetical or ByGroup>; Default: I<ByGroup>.
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435
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436 =item B<IsNucleicAcid>
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437
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438 $Status = IsNucleicAcid($NucleicAcidID);
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439
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440 Returns 1 or 0 based on whether it's a known nucleic acid ID.
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441
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442 =item B<IsNucleicAcidProperty>
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443
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444 $Status = IsNucleicAcid($PropertyName);
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445
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446 Returns 1 or 0 based on whether it's a known nucleic acid property name.
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447
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448 =item B<IsNucleicAcidType>
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449
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450 $Status = IsNucleicAcidType();
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451
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452 Returns 1 or 0 based on whether it's a known nucleic acid type.
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453
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454 =back
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455
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456 =head1 AUTHOR
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457
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458 Manish Sud <msud@san.rr.com>
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459
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460 =head1 SEE ALSO
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461
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462 AminoAcids.pm, PeriodicTable.pm
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463
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464 =head1 COPYRIGHT
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465
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466 Copyright (C) 2015 Manish Sud. All rights reserved.
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467
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468 This file is part of MayaChemTools.
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469
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470 MayaChemTools is free software; you can redistribute it and/or modify it under
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471 the terms of the GNU Lesser General Public License as published by the Free
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472 Software Foundation; either version 3 of the License, or (at your option)
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473 any later version.
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474
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475 =cut
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