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author fgiacomoni
date Fri, 27 Nov 2020 10:06:35 +0000
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1 #!c:\Perl\bin\perl.exe -w
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2
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3 =head1 NAME
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4
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5 bih4bloodexposome.pl - Utility to detect potential contaminants in your peak list based on BloodExposome database
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6
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7 =head1 USAGE
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8
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9
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10 =head1 SYNOPSIS
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11
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12 =head1 DESCRIPTION
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13
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14 =over 4
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15
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16 =item B<function01>
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17
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18 =item B<function02>
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19
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20 =back
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21
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22 =head1 AUTHOR
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23
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24 Prenom Nom E<lt>franck.giacomoni@inrae.frE<gt>
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25
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26 =head1 SUPPORT
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27
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28 You can find documentation for this module with the perldoc command.
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29
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30 perldoc bih4bloodexposome.pl
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31
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32 =head1 LICENSE
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33
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34 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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35
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36 =head1 VERSION
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37
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38 version 0.1.0 : 2020/01/21
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39
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40 version 2 : ??
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41
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42 =cut
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43 #=============================================================================
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44 # Included modules and versions
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45 #=============================================================================
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46 ## Perl modules
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47 use strict ;
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48 use warnings ;
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49 use diagnostics ;
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50 use Carp qw (cluck croak carp) ;
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51
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52 use Data::Dumper ;
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53 use Getopt::Long ;
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54 use File::Basename ;
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55 use FindBin ; ## Allows you to locate the directory of original perl script
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56
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57 ## Specific Perl Modules (PFEM)
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58 use lib $FindBin::Bin ;
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59 my $binPath = $FindBin::Bin ;
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60
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61 ## Dedicate Perl Modules (Home made...)
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62 use Metabolomics::Fragment::Annotation qw( :all ) ;
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63 use Metabolomics::Banks qw( :all ) ;
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64 use Metabolomics::Banks::BloodExposome qw( :all ) ;
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65 use Metabolomics::Utils qw( :all ) ;
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66
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67 ## Initialized values
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68 my $ProgramName = basename($0) ;
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69 my $OptionHelp = undef ;
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70 my $VERBOSE = undef ;
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71
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72 my ($inputFile, $mzCol, $asHeader, $ppmError, $mode ) = (undef, undef, undef, undef, undef, undef, undef ) ;
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73 my ($outputTabular, $outputXls, $outputHTML, $outputFull) = (undef, undef, undef, undef) ;
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74
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75 my $QueryMode = undef ; # depending of the input data the query mode can be ION|NEUTRAL
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76
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77 #=============================================================================
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78 # Manage EXCEPTIONS
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79 #=============================================================================
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80 &GetOptions ( "h|help" => \$OptionHelp, # HELP
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81 "v|verbose=i" => \$VERBOSE, # Level of verbose (0 to 2)
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82 "i|input=s" => \$inputFile, # Input file containing a peak list (mz)
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83 "mzCol=i" => \$mzCol, # Column in CSV file for MZ
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84 "header=i" => \$asHeader, # CSV file as header (1=true, 0=false)
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85 "ppmError=f" => \$ppmError, # ppm error
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86 "m|mode=s" => \$mode, # indicate the ionisation mode (POS|NEG|NEUTRAL)
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87 "outputTab=s" => \$outputTabular, # output file in tabular format
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88 "outputXls=s" => \$outputXls, # output file in Xls format
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89 "outputHtml=s" => \$outputHTML, # output file in html format
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90 "outputFull=s" => \$outputFull, # output file in full format
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91
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92 ) ;
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93
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94 ## if you put the option -help or -h function help is started
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95 if ( defined($OptionHelp) ){ &help ; }
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96
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97 #=============================================================================
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98 # MAIN SCRIPT
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99 #=============================================================================
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100
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101 if ($VERBOSE == 3) {
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102 print "The $ProgramName program is launched as:\n";
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103 print "./$ProgramName " ;
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104 print "--h " if (defined $OptionHelp) ;
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105 print "--input $inputFile " if (defined $inputFile) ;
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106 print "--mzCol $mzCol " if (defined $mzCol) ;
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107 print "--header $asHeader " if (defined $asHeader) ;
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108 print "--ppmError $ppmError " if (defined $ppmError) ;
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109 print "--mode $mode " if (defined $mode) ;
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110 # print "--outputXls $outputXls " if (defined $outputXls) ;
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111 print "--outputTab $outputTabular " if (defined $outputTabular) ;
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112 # print "--outputHtml $outputHTML " if (defined $outputHTML) ;
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113 print "--outputFull $outputFull " if (defined $outputFull) ;
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114 print "with verbose $VERBOSE" ;
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115 print "\n" ;
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116 }
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117
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118 ## Get conf
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119 my ( $oCONF, $oTEMPLATE) = ( undef, undef ) ;
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120 foreach my $conf ( <$binPath/*.cfg> ) { $oCONF = Metabolomics::Utils->utilsAsConf($conf) ; }
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121
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122 foreach my $template ( <$binPath/_template.tabular> ) { $oTEMPLATE = $template ; }
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123
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124 #print Dumper $oCONF ;
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125
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126
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127 if ( ( defined $inputFile ) and ( $inputFile ne "" ) and ( -e $inputFile ) ) {
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128
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129 # create a empty bank object
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130 my $oBank = Metabolomics::Banks::BloodExposome->new() ;
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131
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132 # get contaminants bank
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133 my ($validedMode, $totalEntryNum) = (undef, 0, 0) ;
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134
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135 $oBank->getMetabolitesFromSource() ;
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136
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137 if ( ( defined $mode ) and ( ( $mode eq 'POSITIVE' ) | ( $mode eq 'NEGATIVE' ) | ( $mode eq 'NEUTRAL' ) ) ) {
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138 $validedMode = $mode ;
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139 }
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140 else {
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141 croak "[ERROR] Your ionisation mode is not defined or is different to POSITIVE or NEGATIVE\n"
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142 }
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143
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144 # build the query object
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145 $totalEntryNum = $oBank->buildTheoPeakBankFromEntries($validedMode) ;
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146
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147 # get experimental masses
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148 if ( (defined $mzCol) and (defined $asHeader) ) {
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149 $oBank->parsingMsFragments($inputFile, $asHeader, $mzCol) ;
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150 }
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151
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152 ## Analysis :
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153 my $oAnalysis = Metabolomics::Fragment::Annotation->new($oBank) ;
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154
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155 # print Dumper $oAnalysis ;
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156
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157 # Compare peaklists:
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158 $oAnalysis->compareExpMzToTheoMzList('PPM', $ppmError) ;
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159
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160 # print Dumper $oBank ;
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161
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162
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163
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164 # complete initial input tabular file
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165 if ( (defined $outputFull) and (defined $inputFile) ) {
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166 my $tabularfile = $oAnalysis->writeFullTabularWithPeakBankObject($inputFile, $oTEMPLATE, $outputFull)
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167 }
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168 # write a simple tabular output
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169 if ( (defined $outputTabular) and (defined $inputFile) ) {
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170 my $tabularfile = $oAnalysis->writeTabularWithPeakBankObject($oTEMPLATE, $outputTabular) ;
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171 }
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172 }
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173 else {
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174 croak "Input file is not defined or is not exist.\n" ;
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175 }
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176
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177
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178
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179
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180
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181 #====================================================================================
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182 # Help subroutine called with -h option
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183 # number of arguments : 0
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184 # Argument(s) :
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185 # Return : 1
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186 #====================================================================================
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187 sub help {
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188
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189
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190 print STDERR <<EOF ;
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191 ### $ProgramName ###
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192 #
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193 # AUTHOR: Franck Giacomoni
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194 # VERSION: 1.0
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195 # CREATED: 2019/08/21
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196 # LAST MODIF:
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197 # PURPOSE: This program annotates any known or hypothetical metabolites (peak matching) from ms analysis with BloodExposome database
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198 # USAGE: $ProgramName or $ProgramName --input *.tabular --mzCol INT --header INT --ppmError 5 --mode POSITIVE|NEGATIVE|NEUTRAL --outputTab outTab.tabular --outputFull outFull.tabular --verbose 3
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199 EOF
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200 exit(1) ;
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201 }
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202
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203 ## END of script - F Giacomoni
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204
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205 __END__