diff golm_ws_lib_search.pl @ 0:e3d43b8c987b draft

Init repository with last tool-bank-golm-lib_search master version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/golm_ws_lib_search.pl	Mon Dec 05 08:32:04 2016 -0500
@@ -0,0 +1,375 @@
+#!perl
+
+## script  : XXX.pl
+#=============================================================================
+#                              Included modules and versions
+#=============================================================================
+## Perl modules
+use strict ;
+use warnings ;
+use Carp qw (cluck croak carp) ;
+
+use Data::Dumper ;
+use Getopt::Long ;
+use FindBin ; ## Allows you to locate the directory of original perl script
+
+## Specific Perl Modules (PFEM)
+use lib $FindBin::Bin ;
+my $binPath = $FindBin::Bin ;
+use JSON ;
+
+## Dedicate Perl Modules PFEM
+use lib::golm_ws_api qw( :ALL ) ;
+use lib::msp qw( :ALL ) ;
+use lib::output qw( :ALL ) ;
+use lib::conf qw( :ALL ) ;
+
+## Initialized values
+my ($OptHelp,$ri,$riWindow,$gcColumn,$inputFile,$inputMasses) = (undef,undef,undef,undef,undef,undef) ;
+my ($maxHits,$mzRes,$maxIons,$threshold,$relative,$noise_threshold) = (undef,undef,undef,undef,undef,undef) ;
+my ($JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold) = (undef,undef,undef,undef,undef) ;
+my ($DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) = (undef,undef,undef) ;
+my ($excel_file,$html_file,$html_template,$json_file,$csv_file) = (undef,undef,undef,undef,undef) ;
+my (@hits, @ojson) = ( () , () ) ;
+my $encoded_spectra ;
+
+## if you put no arguments, function help is started
+if (!@ARGV){ &help ; } 
+
+#=============================================================================
+#                                Manage EXCEPTIONS
+#=============================================================================
+&GetOptions ( 	
+				"help|h"     => \$OptHelp,       # HELP
+				"inputFile:s"		=> \$inputFile,
+				"inputMasses:s"		=> \$inputMasses,
+				"ri:i"		=> \$ri,
+				"riWindow:i"		=> \$riWindow,
+				"gcColumn:s"		=> \$gcColumn,
+				"maxHits:i"		=> \$maxHits,
+				"mzRes:i"		=> \$mzRes,
+				"maxIons:i"		=> \$maxIons,
+				#"noiseThreshold:f" => \$noise_threshold,
+				"JaccardDistanceThreshold:f"		=> \$JaccardDistanceThreshold,
+				"s12GowerLegendreDistanceThreshold:f"		=> \$s12GowerLegendreDistanceThreshold,
+				"DotproductDistanceThreshold:f"		=> \$DotproductDistanceThreshold,
+				"HammingDistanceThreshold:f"		=> \$HammingDistanceThreshold,
+				"EuclideanDistanceThreshold:f"		=> \$EuclideanDistanceThreshold,
+				"relative:s"			=> \$relative,
+				"output_xls:s"			=> \$excel_file,
+				"output_html:s"		=> \$html_file,
+				"output_json:s"		=> \$json_file,
+				"output_tabular:s"		=> \$csv_file,
+            ) ;
+            
+            die "maxHits must be >= 0\n" unless ($maxHits >= 0) ;
+            die "mzRes must be >= 0 \n" unless ($mzRes >= 0) ;
+            die "maxIons must be >= 0\n" unless ($maxIons >= 0) ;
+            #die "noiseThreshold must be > 0\n" unless ($noise_threshold > 0) ;
+         
+## if you put the option -help or -h function help is started         
+if(defined($OptHelp)){ &help ; }
+
+if( (!defined ($inputFile)) and (!defined($inputMasses) )){ warn "The input data is not defined (File or mass/intensity list AS string)\n" ; &help ; }
+
+#=============================================================================
+#                                MAIN SCRIPT
+#=============================================================================
+
+## Create module objects ###
+
+my $oapi = lib::golm_ws_api->new() ;
+my $omsp = lib::msp->new() ;
+my $o_output = lib::output->new() ;
+my $oConf = lib::conf->new() ;
+
+
+## -------------- Conf file ------------------------ :
+my ( $CONF ) = ( undef ) ;
+foreach my $conf ( <$binPath/*.cfg> ) {
+	$CONF = $oConf->as_conf($conf) ;
+}
+
+## -------------- HTML template file ------------------------ :
+$html_template = <$binPath/golm_out.tmpl> ;
+$CONF->{'HTML_TEMPLATE'} = $html_template ;
+
+
+## -------------- Retrieve values from conf file ------------------------ :
+my $ws_url = $CONF->{'WS_URL'} ;
+my $ws_proxy = $CONF->{'WS_PROXY'} ;
+my $default_ri = $CONF->{'RI'} ;
+my $default_ri_window = $CONF->{'RI_WINDOW'} ;
+my $default_gc_column = $CONF->{'GC_COLUMN'} ;
+my $default_entries = $CONF->{'DEFAULT_ENTRIES'} ;
+my $analyte_ref = $CONF->{'ANALYTE_REF'} ;
+my $metabolite_ref = $CONF->{'METABOLITE_REF'} ;
+my $spectrum_ref = $CONF->{'SPECTRUM_REF'} ;
+
+############# -------------- Test the Golm web service -------------- ############# :
+
+$oapi->test_query_golm($ws_url, $ws_proxy) ;
+
+############# -------------- Parse the .msp file -------------- ############# :
+
+
+my $ref_mzs_res ;
+my $ref_ints_res ;
+
+## Case when masses are entered manually
+if (defined $inputMasses && !defined $inputFile) { 
+	
+	## Retrieve masses from msp file
+	$ref_mzs_res = $omsp->get_masses_from_string($inputMasses, $mzRes) ;
+	
+	## Retrieve intensities from msp file
+	$ref_ints_res = $omsp->get_intensities_from_string($inputMasses) ;
+	
+	## Sorting intensities
+	my ($mzs_res_sorted, $ints_res_sorted) = $omsp->sorting_descending_intensities($ref_mzs_res, $ref_ints_res) ;
+	
+	#************************
+	# Noise threshold: uncomment if it is not managed in MetaMS 
+	#************************
+	
+	## Apply noise threshold
+	#my ($mzs_res_noise_threshold, $ints_res_noise_threshold) = $omsp->keep_ions_above_threshold($mzs_res_sorted, $ints_res_sorted) ;
+	
+	#************************
+	
+	## Keep a limited number of ions according to $maxIons
+	if($maxIons > 0){
+		
+		## To uncomment if "Apply noise threshold is used"
+		#$ref_mzs_res = $omsp->keep_only_max_masses( $mzs_res_noise_threshold, $maxIons ) ;
+		#$ref_ints_res = $omsp->keep_only_max_intensities( $ints_res_noise_threshold, $maxIons ) ;
+		
+		## To uncomment if "Apply noise threshold is used"
+		$ref_mzs_res = $omsp->keep_only_max_masses( $mzs_res_sorted, $maxIons ) ;
+		$ref_ints_res = $omsp->keep_only_max_intensities( $ints_res_sorted, $maxIons ) ;
+	}
+	
+	## Remove redundant masses
+	my ($uniq_masses , $uniq_intensities) = $omsp->remove_redundants($ref_mzs_res, $ref_ints_res) ;
+	
+	## Relative intensity
+	my $relative_ints_res = undef ;
+	if ($relative eq "true") {
+		my @relative_ints = map { ($_ * 100)/@$ints_res_sorted[0] } @$ints_res_sorted ;
+		$relative_ints_res = \@relative_ints ;
+	}
+	
+	## Encode spectra
+	if (defined $relative_ints_res) {
+		$encoded_spectra = $omsp->encode_spectrum_for_query($mzs_res_sorted, $relative_ints_res) ;
+	}
+	else { $encoded_spectra = $omsp->encode_spectrum_for_query($mzs_res_sorted, $ints_res_sorted) ; }
+	
+}
+## Case with the msp file
+elsif (defined $inputFile and -e $inputFile and !defined $inputMasses and defined $mzRes and defined $maxIons and defined $maxHits) {
+
+	unless (-f $inputFile)  { croak "$inputFile is not a file" ; }
+	unless (-s $inputFile)  { croak "$inputFile is empty" ; }
+	
+	## Get masses and their intensities
+	$ref_mzs_res = $omsp->get_mzs($inputFile, $mzRes) ;
+	$ref_ints_res = $omsp->get_intensities($inputFile, $maxIons) ;
+	
+	## Sorting intensities
+	my ($mzs_res_sorted, $ints_res_sorted) = $omsp->sorting_descending_intensities($ref_mzs_res, $ref_ints_res) ;
+	
+	#************************
+	# Noise threshold: uncomment if it is not managed in MetaMS 
+	#************************
+	
+	## Apply noise threshold if exists
+	#my ($mzs_res_noise_threshold, $ints_res_noise_threshold) = $omsp->keep_ions_above_threshold($mzs_res_sorted, $ints_res_sorted) ;
+	
+	#************************
+	
+	
+	## Keep only $maxIons ions
+	if($maxIons > 0){
+		
+		## To uncomment if "Apply noise threshold is used"
+		#$ref_mzs_res = $omsp->keep_only_max_masses( $mzs_res_noise_threshold, $maxIons ) ;
+		#$ref_ints_res = $omsp->keep_only_max_intensities( $ints_res_noise_threshold, $maxIons ) ;
+		
+		## To uncomment if "Apply noise threshold is used"
+		$mzs_res_sorted = $omsp->keep_only_max_masses( $mzs_res_sorted, $maxIons ) ;
+		$ints_res_sorted = $omsp->keep_only_max_intensities( $ints_res_sorted, $maxIons ) ;
+	}
+	
+	## Remove redundant masses
+	my ($uniq_masses , $uniq_intensities) = (undef,undef) ;
+	my @uniq_total_masses = () ;
+	my @uniq_total_intensities = () ;
+	
+	for (my $i=0 ; $i<@$mzs_res_sorted && $i<@$ints_res_sorted ; $i++) {
+	
+		($uniq_masses , $uniq_intensities) = $omsp->remove_redundants(@$mzs_res_sorted[$i], @$ints_res_sorted[$i]) ;
+		push (@uniq_total_masses , $uniq_masses) ;
+		push (@uniq_total_intensities, $uniq_intensities) ;
+	}
+	
+	## Relative intensity
+	my $relative_ints_res = undef ;
+	if ($relative eq "true") {
+		$relative_ints_res = $omsp->apply_relative_intensity(\@uniq_total_intensities) ;
+	}
+	
+	## Encode spectra
+	if (defined $relative_ints_res) {
+		$encoded_spectra = $omsp->encode_spectrum_for_query(\@uniq_total_masses, $relative_ints_res) ;
+	}
+	else { $encoded_spectra = $omsp->encode_spectrum_for_query(\@uniq_total_masses, \@uniq_total_intensities) ; }
+
+}
+elsif (!defined $maxHits or !defined $maxIons or !defined $mzRes) { croak "Parameters mzRes or maxIons or maxHits are undefined\n"; } 
+elsif (!-f $inputFile) 										  	  { croak "$inputFile does not exist" ; }
+
+############# -------------- Send queries to Golm -------------- ############# :
+
+my $limited_hits ;
+foreach my $spectrum (@$encoded_spectra){
+	($limited_hits) = $oapi->LibrarySearch ($ri, $riWindow, $gcColumn, $spectrum, $maxHits, $JaccardDistanceThreshold,
+																										  $s12GowerLegendreDistanceThreshold,
+																										  $DotproductDistanceThreshold,
+																										  $HammingDistanceThreshold,
+																										  $EuclideanDistanceThreshold,
+																										  $ws_url, $ws_proxy,
+																										  $default_ri, $default_ri_window, $default_gc_column) ;
+	push (@hits , $limited_hits) ;
+}
+			
+
+############# -------------- Build outputs -------------- ############# :
+	
+my $jsons_obj = $o_output->build_json_res_object(\@hits) ;
+#$o_output->write_json_skel(\$json_file, $jsons_obj) ;
+
+# Build the ajax data source for html view
+#my $ajax = $o_output->write_ajax_data_source($jsons_obj) ;
+
+
+my $tbody_entries = $o_output->add_entries_to_tbody_object($jsons_obj,$analyte_ref,$metabolite_ref,$spectrum_ref) ;
+$o_output->write_html_body($jsons_obj, $tbody_entries, $html_file, $html_template, $default_entries, $jsons_obj) ;
+$o_output->excel_like_output($excel_file, $jsons_obj) ;
+$o_output->write_csv($csv_file , $jsons_obj) ;
+
+
+#====================================================================================
+# Help subroutine called with -h option
+# number of arguments : 0
+# Argument(s)        :
+# Return           : 1
+#====================================================================================
+sub help {
+	print STDERR "
+golm_ws_lib_search.pl
+
+# golm_ws_lib_search.pl is a script to use SOAP Golm webservice and send specific queries about spectra searches. 
+# Input : a list of masses (m/z) and their intensities.
+# Authors : Gabriel Cretin / Franck Giacomoni / Yann Guitton 
+# Emails : franck.giacomoni\@clermont.inra.fr
+#		   gabriel.cretin\@clermont.inra.fr
+#		   yann.guitton\@oniris-nantes.fr
+# Version : 1.2
+# Created : 03/06/2016
+# Updated : 28/11/2016
+USAGE :		 
+		golm_ws_lib_search.pl -help OR
+		
+		golm_ws_lib_search.pl 
+			-spectraFile [.msp file]	
+			-spectraMasses [masses + intensities of an ion: 'mz1 int1 mz2 int2 mzx intx...']
+			-ri [Rentention Index: float or integer]
+			-riWindow [Retention Index Window: 1500 or the value of your choice]
+			-gcColumn [AlkaneRetentionIndexGcColumnComposition: 'VAR5' or 'MDN35' or 'None']
+			-maxHits [Maximum hits per queried spectra: integer >= 1 (100 for all of them)]
+			-mzRes [Number of digits after the decimal point for m/z values: integer (0 if none)]
+			-maxIons [Number of m/z per spectra you want to keep for the queries, default 0 for all detected ions]
+			-noiseThreshold [Ions having intensity values less than this value are ignored]
+			-JaccardDistanceThreshold...............[
+			-s12GowerLegendreDistanceThreshold......[  Threshold for each score. Hits with greater scores are ignored: 0 (perfect match) < threshlold <= 1 (mismatch) ]
+			-DotproductDistanceThreshold............[
+			-EuclideanDistanceThreshold.............[
+			-HammingDistanceThreshold[Threshold for hamming score. Hits with greater scores are ignored: 0 - perfect match to higher values indicating a mismatch]
+			-relative [Transforms absolute intensities in the msp file into relative intensities: (intensity * 100)/ max(intensitiess), otherwise, leave them absolute: true or false]
+			-output_xls [name of the xls file in output: string]
+			-output_html [name of the html file in output: string]
+			-output_json [name of the json file in output: string]
+			-output_tabular [name of the csv file in output: string]
+				
+";
+	exit(1);
+}
+
+## END of script
+
+__END__
+
+=head1 NAME
+
+ golm_ws_lib_search.pl -- script to send GC-MS spectra queries to Golm Metabolome Database (GMD)
+
+=head1 USAGE
+
+ golm_ws_lib_search.pl -help OR
+		
+		golm_ws_lib_search.pl 
+			-spectraFile [.msp file]	
+			-spectraMasses [masses + intensities of an ion: 'mz1 int1 mz2 int2 mzx intx...']
+			-ri [Rentention Index: float or integer]
+			-riWindow [Retention Index Window: 1500 or the value of your choice]
+			-gcColumn [AlkaneRetentionIndexGcColumnComposition: 'VAR5' or 'MDN35' or 'None']
+			-maxHits [Maximum hits per queried spectra: integer >= 1 (100 for all of them)]
+			-mzRes [Number of digits after the decimal point for m/z values: integer (0 if none)]
+			-maxIons [Number of m/z per spectra you want to keep for the queries, default 0 for all detected ions]
+			-noiseThreshold [Ions having intensity values less than this value are ignored]
+			-JaccardDistanceThreshold...............[
+			-s12GowerLegendreDistanceThreshold......[  Threshold for each score. Hits with greater scores are ignored: 0 (perfect match) < threshlold <= 1 (mismatch) ]
+			-DotproductDistanceThreshold............[
+			-EuclideanDistanceThreshold.............[
+			-HammingDistanceThreshold[Threshold for hamming score. Hits with greater scores are ignored: 0 - perfect match to higher values indicating a mismatch]
+			-relative [Transforms absolute intensities in the msp file into relative intensities: (intensity * 100)/ max(intensitiess), otherwise, leave them absolute: true or false]
+			-output_xls [name of the xls file in output: string]
+			-output_html [name of the html file in output: string]
+			-output_json [name of the json file in output: string]
+			-output_tabular [name of the csv file in output: string]
+
+=head1 SYNOPSIS
+
+This script sends GC-MS EI spectra from an msp file given in argument to Golm Database, and presents results on a web interface.
+
+=head1 DESCRIPTION
+
+This main program is a ...
+
+=over 4
+
+=item B<function01>
+
+=item B<function02>
+
+=back
+
+=head1 AUTHOR
+
+Gabriel Cretin	E<lt>[e-mail]<gt>
+Franck Giacomoni E<lt>[e-mail]<gt>
+
+=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 1.0 : 03 / 06 / 2016
+
+version 1.1 : 24 / 06 / 2016
+
+version 1.2 : 28 / 11 / 2016
+
+=cut
\ No newline at end of file