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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 bih4maconda.pl - Utility to detect potential contaminants in your peak list based on MaConDa 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@inra.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 bih4maconda.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 1 : 2019/07/24
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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::Banks::MaConDa qw( :all ) ;
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66 use Metabolomics::Banks::AbInitioFragments qw( :all ) ;
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67 use Metabolomics::Utils qw( :all ) ;
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68
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69 ## Initialized values
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70 my $ProgramName = basename($0) ;
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71 my $OptionHelp = undef ;
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72 my $VERBOSE = undef ;
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73
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74 my ($inputFile, $mzCol, $asHeader, $ppmError, $mode, $instruments, $instrumentTypes) = (undef, undef, undef, undef, undef, undef, undef ) ;
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75 my ($outputTabular, $outputXls, $outputHTML, $outputFull) = (undef, undef, undef, undef) ;
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76
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77 my $QueryMode = undef ; # depending of the input data the query mode can be ION|NEUTRAL
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78
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79 #=============================================================================
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80 # Manage EXCEPTIONS
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81 #=============================================================================
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82 &GetOptions ( "h|help" => \$OptionHelp, # HELP
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83 "v|verbose=i" => \$VERBOSE, # Level of verbose (0 to 2)
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84 "i|input=s" => \$inputFile, # Input file containing a peak list (mz)
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85 "mzCol=i" => \$mzCol, # Column in CSV file for MZ
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86 "header=i" => \$asHeader, # CSV file as header (1=true, 0=false)
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87 "ppmError=f" => \$ppmError, # ppm error
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88 "m|mode=s" => \$mode, # indicate the ionisation mode (POS|NEG|NEUTRAL)
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89 "filterInstrument=s" => \$instruments, # instruments listing to apply filter
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90 "filterInstrumentType=s" => \$instrumentTypes, # instrumentTypes listing to apply filter
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91 "outputTab=s" => \$outputTabular, # output file in tabular format
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92 "outputXls=s" => \$outputXls, # output file in Xls format
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93 "outputHtml=s" => \$outputHTML, # output file in html format
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94 "outputFull=s" => \$outputFull, # output file in full format
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95
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96 ) ;
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97
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98 ## if you put the option -help or -h function help is started
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99 if ( defined($OptionHelp) ){ &help ; }
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100
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101 #=============================================================================
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102 # MAIN SCRIPT
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103 #=============================================================================
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104
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105 if ($VERBOSE == 3) {
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106 print "The $ProgramName program is launched as:\n";
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107 print "./$ProgramName " ;
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108 print "--h " if (defined $OptionHelp) ;
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109 print "--input $inputFile " if (defined $inputFile) ;
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110 print "--mzCol $mzCol " if (defined $mzCol) ;
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111 print "--header $asHeader " if (defined $asHeader) ;
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112 print "--ppmError $ppmError " if (defined $ppmError) ;
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113 print "--mode $mode " if (defined $mode) ;
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114 print "--filterInstrument $instruments " if (defined $instruments) ;
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115 print "--filterInstrumentType $instrumentTypes " if (defined $instrumentTypes) ;
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116 # print "--outputXls $outputXls " if (defined $outputXls) ;
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117 print "--outputTab $outputTabular " if (defined $outputTabular) ;
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118 # print "--outputHtml $outputHTML " if (defined $outputHTML) ;
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119 print "--outputFull $outputFull " if (defined $outputFull) ;
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120 print "with verbose $VERBOSE" ;
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121 print "\n" ;
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122 }
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123
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124 ## Get conf
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125 my ( $oCONF, $oTEMPLATE) = ( undef, undef ) ;
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126 foreach my $conf ( <$binPath/*.cfg> ) { $oCONF = Metabolomics::Utils->utilsAsConf($conf) ; }
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127
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128 foreach my $template ( <$binPath/_template.tabular> ) { $oTEMPLATE = $template ; }
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129
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130 #print Dumper $oCONF ;
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131
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132
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133 if ( ( defined $inputFile ) and ( $inputFile ne "" ) and ( -e $inputFile ) ) {
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134
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135 # create a empty bank object
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136 my $oBank = Metabolomics::Banks::MaConDa->new() ;
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137
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138 # get contaminants bank
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139 my ($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = (undef, 0, 0) ;
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140
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141 $oBank->getContaminantsExtensiveFromSource() ;
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142
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143 # Applying filters
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144
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145 ## Instrument #Filter01 (ALL|...)
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146 if ( defined $instruments ) {
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147 my @instruments = split(/,/, $instruments) ;
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148 ($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = $oBank->filterContaminantInstruments(\@instruments) ;
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149 print "Only few instruments were selected: $fiteredEntryNum/$totalEntryNum entries were filtered.\n" ;
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150 }
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151 ## Instrument type #Filter02 (ALL|...)
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152 if ( defined $instrumentTypes ) {
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153
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154 my @instrumentTypes = split(/,/, $instrumentTypes) ;
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155 if (!defined $oFilteredContaminants){ ($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = $oBank->filterContaminantInstrumentTypes(\@instrumentTypes) ; }
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156 else { ($oFilteredContaminants, $totalEntryNum, $fiteredEntryNum) = $oFilteredContaminants->filterContaminantInstrumentTypes(\@instrumentTypes) ; }
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157
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158 print "Only few instrument types were selected: $fiteredEntryNum/$totalEntryNum entries were filtered.\n" ;
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159 }
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160 ## Ion mode #Filter03 (POS|NEG|BOTH)
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161 if ( defined $mode) {
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162
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163 print "Mode selected is $mode..." ;
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164
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165 if (!defined $oFilteredContaminants){ $oFilteredContaminants = $oBank->filterContaminantIonMode($mode) ; }
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166 else { $oFilteredContaminants = $oFilteredContaminants->filterContaminantIonMode($mode) ; }
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167
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168 if ( ($mode eq 'POSITIVE') or ($mode eq 'NEGATIVE') or ($mode eq 'BOTH') ) {
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169 $QueryMode = 'ION' ;
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170 }
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171 elsif ($mode eq 'NEUTRAL') {
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172 $QueryMode = 'NEUTRAL' ;
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173 }
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174 else {
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175 croak "[ERROR] mode $mode is not recognize...Please defined a acceptable one\n" ;
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176 }
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177 print "and detected query mode is $QueryMode...\n" ;
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178 }
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179 # in case no filter is defined beforr
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180 if ( ( !defined $mode) and ( !defined $instruments) and ( !defined $instrumentTypes) ) {
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181 $oFilteredContaminants = $oBank ;
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182 }
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183
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184 # build the query object
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185 $oFilteredContaminants->buildTheoPeakBankFromContaminants($QueryMode) ;
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186
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187 # get experimental masses
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188 if ( (defined $mzCol) and (defined $asHeader) ) {
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189 $oFilteredContaminants->parsingMsFragments($inputFile, $asHeader, $mzCol) ;
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190 }
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191
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192 ## Analysis :
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193 my $oAnalysis = Metabolomics::Fragment::Annotation->new($oFilteredContaminants) ;
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194
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195
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196 # Compare peaklists:
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197 $oAnalysis->compareExpMzToTheoMzList('PPM', $ppmError) ;
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198
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199 # print Dumper $oBank ;
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200
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201
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202
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203 # complete initial input tabular file
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204 if ( (defined $outputFull) and (defined $inputFile) ) {
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205 my $tabularfile = $oAnalysis->writeFullTabularWithPeakBankObject($inputFile, $oTEMPLATE, $outputFull)
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206 }
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207 # write a simple tabular output
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208 if ( (defined $outputTabular) and (defined $inputFile) ) {
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209 my $tabularfile = $oAnalysis->writeTabularWithPeakBankObject($oTEMPLATE, $outputTabular) ;
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210 }
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211 }
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212 else {
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213 croak "Input file is not defined or is not exist.\n" ;
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214 }
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215
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216
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217
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218
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219
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220 #====================================================================================
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221 # Help subroutine called with -h option
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222 # number of arguments : 0
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223 # Argument(s) :
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224 # Return : 1
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225 #====================================================================================
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226 sub help {
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227
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228
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229 print STDERR <<EOF ;
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230 ### $ProgramName ###
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231 #
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232 # AUTHOR: Franck Giacomoni
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233 # VERSION: 1.0
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234 # CREATED: 2019/08/21
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235 # LAST MODIF:
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236 # PURPOSE: This program annotates any known contaminants from ms analysis depending some filters as instruments, ionisation mode from MaConDa database
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237 # 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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238 EOF
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239 exit(1) ;
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240 }
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241
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242 ## END of script - F Giacomoni
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243
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244 __END__ |
