--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bih4bloodexposome.pl	Fri Nov 27 10:06:35 2020 +0000
@@ -0,0 +1,205 @@
+#!c:\Perl\bin\perl.exe -w
+
+=head1 NAME
+
+bih4bloodexposome.pl - Utility to detect potential contaminants in your peak list based on BloodExposome database
+
+=head1 USAGE
+
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=over 4
+
+=item B<function01>
+
+=item B<function02>
+
+=back
+
+=head1 AUTHOR
+
+Prenom Nom E<lt>franck.giacomoni@inrae.frE<gt>
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+ perldoc bih4bloodexposome.pl
+
+=head1 LICENSE
+
+This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
+
+=head1 VERSION
+
+version 0.1.0 : 2020/01/21
+
+version 2 : ??
+
+=cut
+#=============================================================================
+#                              Included modules and versions
+#=============================================================================
+## Perl modules
+use strict ;
+use warnings ;
+use diagnostics ;
+use Carp qw (cluck croak carp) ;
+
+use Data::Dumper ;
+use Getopt::Long ;
+use File::Basename ;
+use FindBin ; ## Allows you to locate the directory of original perl script
+
+## Specific Perl Modules (PFEM)
+use lib $FindBin::Bin ;
+my $binPath = $FindBin::Bin ;
+
+## Dedicate Perl Modules (Home made...)
+use Metabolomics::Fragment::Annotation qw( :all ) ;
+use Metabolomics::Banks qw( :all ) ;
+use Metabolomics::Banks::BloodExposome qw( :all ) ;
+use Metabolomics::Utils qw( :all ) ;
+
+## Initialized values
+my $ProgramName = basename($0) ;
+my $OptionHelp = undef ;
+my $VERBOSE = undef ;
+
+my ($inputFile, $mzCol, $asHeader, $ppmError, $mode ) = (undef, undef, undef, undef, undef, undef, undef ) ;
+my ($outputTabular, $outputXls, $outputHTML, $outputFull) = (undef, undef, undef, undef) ;
+
+my $QueryMode = undef ; # depending of the input data the query mode can be ION|NEUTRAL
+
+#=============================================================================
+#                                Manage EXCEPTIONS
+#=============================================================================
+&GetOptions ( 	"h|help"     => \$OptionHelp,       # HELP
+				"v|verbose=i"	=> \$VERBOSE,		# Level of verbose (0 to 2)
+				"i|input=s"		=> \$inputFile, 		# Input file containing a peak list (mz)
+				"mzCol=i"		=> \$mzCol,				# Column in CSV file for MZ
+				"header=i"		=> \$asHeader,				# CSV file as header (1=true, 0=false)
+				"ppmError=f"	=> \$ppmError,				# ppm error
+				"m|mode=s"		=> \$mode,				# indicate the ionisation mode (POS|NEG|NEUTRAL)
+				"outputTab=s"		=> \$outputTabular,			# output file in tabular format
+				"outputXls=s"		=> \$outputXls,			# output file in Xls format
+				"outputHtml=s"		=> \$outputHTML,			# output file in html format
+				"outputFull=s"		=> \$outputFull,			# output file in full format
+				
+            ) ;
+         
+## if you put the option -help or -h function help is started
+if ( defined($OptionHelp) ){ &help ; }
+
+#=============================================================================
+#                                MAIN SCRIPT
+#=============================================================================
+
+if ($VERBOSE == 3) {
+	print "The $ProgramName program is launched as:\n";
+	print "./$ProgramName " ;
+	print "--h "  if (defined $OptionHelp) ;
+	print "--input $inputFile " if (defined $inputFile) ;
+	print "--mzCol $mzCol " if (defined $mzCol) ;
+	print "--header $asHeader " if (defined $asHeader) ;
+	print "--ppmError $ppmError " if (defined $ppmError) ;
+	print "--mode $mode " if (defined $mode) ;
+#	print "--outputXls $outputXls " if (defined $outputXls) ;
+	print "--outputTab $outputTabular " if (defined $outputTabular) ;
+#	print "--outputHtml $outputHTML " if (defined $outputHTML) ;
+	print "--outputFull $outputFull " if (defined $outputFull) ;
+	print "with verbose $VERBOSE" ;
+	print "\n" ;	
+}
+
+## Get conf
+my ( $oCONF, $oTEMPLATE) = ( undef, undef ) ;
+foreach my $conf ( <$binPath/*.cfg> ) { $oCONF = Metabolomics::Utils->utilsAsConf($conf) ; }
+
+foreach my $template ( <$binPath/_template.tabular> ) { $oTEMPLATE = $template ; }
+
+#print Dumper $oCONF ;
+
+
+if ( ( defined $inputFile ) and ( $inputFile ne "" ) and ( -e $inputFile ) ) {
+	
+	# create a empty bank object
+	my $oBank = Metabolomics::Banks::BloodExposome->new() ;
+	
+	# get contaminants bank
+	my ($validedMode, $totalEntryNum) = (undef, 0, 0) ;
+	
+	$oBank->getMetabolitesFromSource() ;
+	
+	if ( ( defined $mode ) and  ( ( $mode eq 'POSITIVE' ) | ( $mode eq 'NEGATIVE' ) | ( $mode eq 'NEUTRAL' ) ) ) {
+		$validedMode = $mode ;
+	}
+	else {
+		croak "[ERROR] Your ionisation mode is not defined or is different to POSITIVE or NEGATIVE\n"
+	}
+
+	# build the query object
+	$totalEntryNum = $oBank->buildTheoPeakBankFromEntries($validedMode) ;
+	
+	# get experimental masses
+	if ( (defined $mzCol) and (defined $asHeader) ) {
+		$oBank->parsingMsFragments($inputFile, $asHeader, $mzCol) ;
+	}
+	
+	## Analysis :
+	my $oAnalysis = Metabolomics::Fragment::Annotation->new($oBank) ;
+	
+#	print Dumper $oAnalysis ;
+
+	# Compare peaklists:
+	$oAnalysis->compareExpMzToTheoMzList('PPM', $ppmError) ;
+	
+#	print Dumper $oBank ;
+	
+	
+	
+	# complete initial input tabular file
+	if ( (defined $outputFull) and (defined $inputFile) ) {
+		my $tabularfile = $oAnalysis->writeFullTabularWithPeakBankObject($inputFile, $oTEMPLATE, $outputFull)
+	}
+	# write a simple tabular output
+	if ( (defined $outputTabular) and (defined $inputFile) ) {
+		my $tabularfile = $oAnalysis->writeTabularWithPeakBankObject($oTEMPLATE, $outputTabular) ;
+	}
+}
+else {
+	croak "Input file is not defined or is not exist.\n" ;
+}
+
+
+
+
+
+#====================================================================================
+# Help subroutine called with -h option
+# number of arguments : 0
+# Argument(s)        :
+# Return           : 1
+#====================================================================================
+sub help {
+
+
+print STDERR <<EOF ;
+### $ProgramName ###
+#
+# AUTHOR:     Franck Giacomoni
+# VERSION:    1.0
+# CREATED:    2019/08/21
+# LAST MODIF: 
+# PURPOSE: This program annotates any known or hypothetical metabolites (peak matching) from ms analysis with BloodExposome database 
+# USAGE: $ProgramName or $ProgramName --input *.tabular --mzCol INT --header INT --ppmError 5 --mode POSITIVE|NEGATIVE|NEUTRAL --outputTab outTab.tabular --outputFull outFull.tabular --verbose 3 
+EOF
+exit(1) ;
+}
+
+## END of script - F Giacomoni 
+
+__END__
\ No newline at end of file