diff bank_inhouse.pl @ 0:be582bcd6585 draft

Master branch Updating - - Fxx

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bank_inhouse.pl	Thu Oct 04 10:37:14 2018 -0400
@@ -0,0 +1,493 @@
+#!perl
+
+## script  : bank_inhouse.pl
+#=============================================================================
+#                              Included modules and versions
+#=============================================================================
+## Perl modules
+use strict ;
+use warnings ;
+use Carp qw (cluck croak carp) ;
+
+use Data::Dumper ;
+use Getopt::Long ;
+use POSIX ;
+use List::Util qw( min max );
+use FindBin ; ## Allows you to locate the directory of original perl script
+
+## Specific Modules
+use lib $FindBin::Bin ;
+my $binPath = $FindBin::Bin ;
+use lib::bih qw( :ALL ) ;
+
+## PFEM Perl Modules
+use lib::conf  qw( :ALL ) ;
+use lib::csv  qw( :ALL ) ;
+
+## Initialized values
+my ( $help ) = ( undef ) ;
+my ( $mass ) = ( undef ) ;
+my ( $masses_file, $nbline_header, $col_mass ) = ( undef, undef, undef ) ;
+my ( $col_rt, $manual_rt, $rt_delta, $mz_delta_type, $mz_delta, $rtdb ) = ( undef, undef, undef, undef, undef, undef ) ;
+my ( $mode, $tissues, $bank_in, $bank_name, $col_mzdb) = ( undef, undef, undef, undef, undef ) ;
+my ( $out_tab, $out_html, $out_xls, $out_json, $out_full ) = ( undef, undef, undef, undef, undef ) ;
+my ($rest_mode) = ('no') ;
+
+my ( $verbose ) = ( 2 ) ; ## verbose level is 3 for debugg
+
+#=============================================================================
+#                                Manage EXCEPTIONS
+#=============================================================================
+
+&GetOptions ( 	"h"					=> \$help,				# HELP
+				"masse:s"			=> \$mass,				## option : one masse
+				"input:s"			=> \$masses_file,		## option : path to the input
+				"rest:s"			=> \$rest_mode,			## option : allow uses of peakforest rest service 
+				"nbheader:i"		=> \$nbline_header,		## numbre of header line present in file
+				"colrt:i"			=> \$col_rt,			## Column retention time for retrieve formula/masses list in tabular file
+				"rt:s"				=> \$manual_rt,			## Retention time for manual masses list
+				"rt_delta:f"		=> \$rt_delta,			## Delta for retention time
+				"colmass:i"			=> \$col_mass,			## Column id for retrieve formula list in tabular file
+				"mz_delta:s"		=> \$mz_delta_type,		## Delta type for masses
+				"mass_delta:f"		=> \$mz_delta,			## Delta for masses
+				"mode:s"			=> \$mode,				## Molecular species (positive/negative/neutral) 
+				"tissues:s"			=> \$tissues,			## Restricted to certain characterization and localization (blood/plasma/urine/peptide) 
+				"bank_in:s"			=> \$bank_in,			## option : path to a personal data bank
+				"bank_name:s"		=> \$bank_name,			## option : name of the bank
+				"mzdb:i"			=> \$col_mzdb,			## Column number in which is the masses of the personal data bank
+				"rtdb:i"			=> \$rtdb,				## Column number in which is the retention time of the personal data bank
+				"outputJson:s"		=> \$out_json,			## option : path to the ouput (results)
+				"outputXls:s"		=> \$out_xls,			## option : path to the ouput (tabular : results )
+				"outputTab:s"		=> \$out_tab,			## path to the ouput (tabular : input+results (1 col) )
+				"outputView:s"		=> \$out_html,			## option : path to the results view (output2)
+				"outputFull:s"		=> \$out_full,			## path to the ouput (tabular : input+results (x col) )
+			) ;
+
+#=============================================================================
+#                                EXCEPTIONS
+#=============================================================================
+## if you put the option -help or -h function help is started
+if ( defined $help ) { &help() ; }
+
+#=============================================================================
+#                                MAIN SCRIPT
+#=============================================================================
+
+
+print "The bank_inhouse program is launched as:\n";
+print "./bank_inhouse.pl " ;
+print "--h "  if (defined $help) ;
+print "--masse $mass " if (defined $mass) ;
+print "--input $masses_file " if (defined $masses_file) ;
+print "--rest $rest_mode " if (defined $rest_mode) ;
+print "--nbheader $nbline_header " if (defined $nbline_header) ;
+print "--colrt $col_rt " if (defined $col_rt) ;
+print "--rt $manual_rt " if (defined $manual_rt) ;
+print "--colmass $col_mass " if (defined $col_mass) ;
+print "--mz_delta $mz_delta_type " if (defined $mz_delta_type) ;
+print "--mass_delta $mz_delta " if (defined $mz_delta) ;
+print "--mode $mode " if (defined $mode) ;
+print "--tissues $tissues " if (defined $tissues) ;
+print "--bank_in $bank_in " if (defined $bank_in) ;
+print "--bank_name $bank_name " if (defined $bank_name) ;
+print "--mzdb $col_mzdb " if (defined $col_mzdb) ;
+print "--rtdb $rtdb " if (defined $rtdb) ;
+print "--outputJson $out_json " if (defined $out_json) ;
+print "--outputXls $out_xls " if (defined $out_xls) ;
+print "--outputTab $out_tab " if (defined $out_tab) ;
+print "--outputView $out_html " if (defined $out_html) ;
+print "--outputFull $out_full " if (defined $out_full) ;
+print "\n" ;
+
+
+
+## -------------- Conf file ------------------------ :
+my ( $CONF, $PF_CONF ) = ( undef, undef ) ;
+foreach my $conf ( <$binPath/*.cfg> ) {
+	my $oConf = lib::conf::new() ;
+	$CONF = $oConf->as_conf($conf) ;
+}
+
+## PForest dedicated conf
+if ((defined $rest_mode ) and ( $rest_mode eq "yes" )) {
+	foreach my $ini ( <$binPath/*.ini> ) {
+		my $oConf = lib::conf::new() ;
+		$PF_CONF = $oConf->as_conf($ini) ;
+	}
+}
+
+## --------------- Global parameters ---------------- :
+my ( $masses, $rt, $results, $header_choice ) = ( undef, undef, undef, undef, undef ) ; ##############
+my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ;
+
+my $oBih = lib::bih::new() ;
+
+## --------------- retrieve input data -------------- :
+
+## manage manual mass(es)
+if ( ( defined $mass ) and ( $mass ne "" ) ) {
+	$mass =~ tr/,/./ ;
+	@$masses = split(' ', $mass);
+	if  ( ( defined $manual_rt ) and ( $manual_rt ne "" ) ) {
+		$manual_rt =~ tr/,/./ ;
+		@$rt = split(' ', $manual_rt) ;
+		if  ( $#$rt != $#$masses) {	croak "You have not given the same number of masses and retention time\n" ;	}
+	}
+} ## END IF
+
+## manage csv file containing list of masses
+elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) {
+	## parse all csv for later : output csv build
+	my $ocsv_input  = lib::csv->new() ;
+	my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
+	$complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ;
+	
+	## parse csv ids and masses
+	my $ocsv = lib::csv->new() ;
+	my $csv = $ocsv->get_csv_object( "\t" ) ;
+	if ( ( defined $nbline_header ) and ( $nbline_header > 0 ) ) { $header_choice = 'yes' ; }	else{ $header_choice = 'no' ; }
+	$masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv
+	if  ( ( defined $col_rt ) and ( $col_rt ne "" ) ) {
+		$rt = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_rt, $header_choice, $nbline_header ) ; ## retrieve rt values on csv
+	}
+}
+
+# --------------- retrieve personal data bank input -------------- :
+
+my ($complete_bank, $bank_head) = (undef, undef) ;
+
+## check up $bank_in and parse
+if ( ( defined $bank_in ) and ( $bank_in ne '' ) and ( -e $bank_in ) and ( defined $col_mzdb ) and ( $col_mzdb ne '' ) ) {
+	## parse csv bank_in
+	my $ocsv_input  = lib::csv->new() ;
+	my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
+	($complete_bank, $bank_head)= $oBih->parse_bank_interest($complete_csv, \$bank_in, $col_mzdb-1) ;
+}
+## manage rest service of PeakForest and set $masses and $rt with given databases
+elsif  ( ( defined $rest_mode ) and ( $rest_mode eq "yes" ) ) {
+	$bank_name = "PeakForest";
+	if ( ( $PF_CONF->{PF_GLOBAL_TOKEN} ne "" ) and ( $PF_CONF->{PF_WS_URL} ne "" ) ) {
+		## init
+		my $opfws = lib::bih::new() ;
+		## get min and max values of user query
+		my ($min, $max) = (0, 0) ;
+			
+		if ( ( defined $masses ) and ( scalar (@{$masses}) > 0 ) ) {
+			$min = min @{$masses} ;
+			$max = max @{$masses} ;
+#			print Dumper $masses ;
+			## TODO: adjust min and max with delta
+			my ( $min_delta, undef ) = $opfws->mz_delta_conversion(\$min, \$mz_delta_type, \$mz_delta) ;
+			my ( undef, $max_delta ) = $opfws->mz_delta_conversion(\$max, \$mz_delta_type, \$mz_delta) ;
+
+			## get clean range database json from PForest WS : 
+			my $pf_json = $opfws->db_pforest_get_clean_range($PF_CONF->{PF_WS_URL}, $PF_CONF->{PF_REST_QUERY_CLEAN_RANGE}, $$min_delta, $$max_delta, $mode) ;
+			if (defined $pf_json) {
+				($complete_bank, $bank_head) = $opfws->map_pfjson_bankobject($pf_json) ;
+			}
+		} ## End IF
+		else {
+			croak "Fatal error : your mass list is empty\n" ;
+		}
+	} ## End IF PForest param
+	else {	croak "Can't work : missing a PForest REST paramater\n" ;	}
+} ## End ELSIF PForest
+elsif ( ( defined $CONF->{'INHOUSE_BANK'} ) and ( $CONF->{'INHOUSE_BANK'} ne '' ) ) {
+	$col_mzdb = 4;
+	$bank_name = "internal_bank";
+	if  ( (defined $col_rt) or (defined $manual_rt) or (defined $rt_delta) ) {	croak "No retention time in the internal bank, please use your own bank\n" ;	}
+	my $html_file = $binPath.'/'.$CONF->{'INHOUSE_BANK'} ;
+	if ( -e $html_file ) {
+		## parse all csv for later : output csv build
+		my $ocsv_input  = lib::csv->new() ;
+		my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
+		($complete_bank, $bank_head)= $oBih->parse_bank_interest($complete_csv, \$html_file, $col_mzdb-1) ;
+	}
+	else {	croak "Can't work : no local inhouse bank name '$html_file'\n" ;	}
+}
+else {	croak "Can't work : missing an inhouse bank\n" ;	}
+
+## ---------------- launch queries -------------------- :
+
+my $ionization = undef ;
+my $characterization = undef ;
+my $valH = undef ;
+my $bank = undef ;
+my $search_condition = undef ;
+
+#($valH, $ionization)= $oBih->manage_mode($mode, $CONF->{'PROTON_MZ'}, $CONF->{'ELECTRON_MZ'}) ;
+
+######### Manage Tissues ##############################################################################
+#if ( ( !defined $tissues ) or ( $tissues eq '' ) or ( $tissues eq 'none' ) ) {
+#	$characterization = ['None'];
+#} else {	@{$characterization} = split(",", $tissues);	}
+######### End #########################################################################################
+
+#if ( (@$ionization = (['None'])) and (@$characterization = (['None']))) {	$bank = $complete_bank;	}
+#else  {	$bank = FILTER LA BANK;	}
+$bank = $complete_bank;
+$valH = 0 ;
+
+#if ( ( defined $mz_delta ) and ( $mz_delta > 0 ) and ( defined $ionization ) and ( defined $characterization ) and ( defined $masses ) and ( defined $ids ) and ( defined $bank ) ) {
+#	$search_condition = "Search params : Molecular specie = $mode / delta = $mz_delta / characterization and localization = $tissues \n bank file = $bank_in" ;
+
+if ( ( defined $mz_delta ) and ( $mz_delta >= 0 ) and ( defined $masses ) and ( defined $bank ) ) {
+	## prepare masses list and execute query
+	$results = [] ;
+	if ($mz_delta != 0){
+		my @sort_masses_bank = sort { $a <=> $b } keys(%$bank);
+		
+		my $compt_masses = 0;
+		foreach my $mz (@$masses) {
+			$compt_masses++;
+			my ($MZmessage) = $oBih->check_interval($mz, 0, 10000) ;
+			if ( $MZmessage eq 'OK' ){
+				my ( $min, $max ) = $oBih->mz_delta_conversion(\$mz, \$mz_delta_type, \$mz_delta) ;
+				
+				my ($marj_inf) = $oBih->dichotomi_search(\@sort_masses_bank, $min) ;
+				my ($marj_sup) = $oBih->dichotomi_search(\@sort_masses_bank, $max) ;
+				
+				my $result = [];
+				if($$marj_inf != $$marj_sup){
+					if ($$marj_inf == -1){	$$marj_inf=0;	}
+					for (my $i=$$marj_inf; $i<$$marj_sup; $i++){
+						my $bank_tmp = $$bank{$sort_masses_bank[$i]};
+						if  ( ( defined $rt ) and ( $rt ne "" ) ) {
+							my ($RTmessage) = $oBih->check_interval($$rt[$compt_masses-1], 0, 60) ;
+							if ( $RTmessage eq 'OK' ){
+								my $bank_rt = [];
+								for(my $nb_rt=0; $nb_rt<=$#$bank_tmp; $nb_rt++){
+									my ($RTbank) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], 0, 60) ;
+									my ($RTsearch) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], $$rt[$compt_masses-1]-$rt_delta, $$rt[$compt_masses-1]+$rt_delta) ;
+									if ( ($RTbank eq 'OK') and ($RTsearch eq 'OK') ){
+										push (@$result, $bank_tmp->[$nb_rt]) ;
+									}
+									elsif ($RTbank ne 'OK'){	croak "At least one retention time in bank is not valid : $RTbank\n" ;	}
+								}
+							}
+							else {	croak "The $compt_masses th analyzed retention time : $RTmessage\n" ;	}
+						}
+						else {	push (@$result, @$bank_tmp) ;	}
+					}
+				}
+				else{	$result = [];	}
+				push (@$results, [@$result]) ;
+			}
+			else {	croak "The $compt_masses th value : $MZmessage\n" ;	}
+			print Dumper $results if ($verbose>2) ;
+		} ## End FOREACH MZ queried
+	} ## End IF
+	else{
+		my $result = [];
+		my $compt_masses = 0;
+		foreach my $mz (@$masses) {
+			$compt_masses++;
+			my ($MZmessage) = $oBih->check_interval($mz, 0, 10000) ;
+			if ( $MZmessage eq 'OK' ){
+				if ($$bank{$mz}){
+					my $bank_tmp = $$bank{$mz};
+					if  ( ( defined $rt ) and ( $rt ne "" ) ) {
+						my ($RTmessage) = $oBih->check_interval($$rt[$compt_masses-1], 0, 60) ;
+						if ( $RTmessage eq 'OK' ){my $bank_rt = [];
+							for(my $nb_rt=0; $nb_rt<=$#$bank_tmp; $nb_rt++){
+								my ($RTbank) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], 0, 60) ;
+								my ($RTsearch) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], $$rt[$compt_masses-1]-$rt_delta, $$rt[$compt_masses-1]+$rt_delta) ;
+								if ( ($RTbank eq 'OK') and ($RTsearch eq 'OK') ){
+									push (@$bank_rt, $bank_tmp->[$nb_rt]) ;
+								}
+								elsif ($RTbank ne 'OK'){	croak "At least one retention time in bank is not valid : $RTbank\n" ;	}
+							}
+							if ($#$bank_rt>=0){		## If there is at least one result
+								push (@$result, $bank_rt) ;
+							}	## else $bank_rt = [] as defined
+						}
+						else {	croak "The $compt_masses th analyzed retention time : $RTmessage\n" ;	}
+					}
+					else {	push (@$result, [$bank_tmp]) ;	}
+				}
+				else {	push (@$result, [] ) ;	}
+			}
+			else {	croak "The $compt_masses th mass : $MZmessage\n" ;	}
+		}
+		$results = [@$results, @$result] ;
+	}
+}
+else {
+	croak "Can't work : missing paramaters (list of ids, masses, delta, ionization, characterization or inhouse_bank)\n" ;
+} ## end ELSE
+
+
+if  ( ( defined $rt ) and ( $rt ne "" ) ) {	unshift (@$bank_head, ("DELTA_mass(".$mz_delta.$mz_delta_type.")", "MASS_Result", "DELTA_RT(".$rt_delta.")", "RT_Result")) ;	}
+else {	unshift (@$bank_head, ("DELTA_mass(".$mz_delta.$mz_delta_type.")", "MASS_Result")) ;	}
+
+
+## -------------- Produce JSON output ------------------ :
+if ( ( defined $out_json ) and ( defined $results ) ) {
+	open(JSON, '>:utf8', "$out_json") or die "Cant' create the json file\n" ;
+	print JSON Dumper $results;
+	close(JSON) ;
+} ## END IF
+else {
+	#croak "Can't create a json output for Massbank : no result found or your output file is not defined\n" ;
+}
+
+## -------------- Produce HTML output ------------------ :
+
+#if ( ( defined $out_html ) and ( defined $results ) ) {
+#	## Uses N mz and theirs entries per page (see config file).
+#	# how many pages you need with your input mz list?
+#	$nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} )  ;
+#	
+#	my $oHtml = lib::bih::new() ;
+#	my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
+#	($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
+#	($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
+#	print Dumper $tbody_object;exit;
+#	my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ;
+#	
+#} ## END IF
+#else {	croak "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ;	}
+
+## -------------- Produce XLS like output ------------------ :
+if ( ( defined $out_xls ) and ( defined $results ) ) {
+	my $oxls = lib::bih::new() ;
+	$oxls->write_excel_like_mass($masses, $mz_delta_type, $mz_delta, $col_mzdb, $rt, $rt_delta, $rtdb, $results, $out_xls, $bank_head) ;
+} ## END IF
+else {	croak "Can't create a tabular output for BiH (like xls): no result found or your output file is not defined\n" ;	}
+
+## -------------- Produce CSV output ------------------ :
+if (defined $results) {
+	if ( defined $masses_file ) {	# produce a csv based on METLIN format
+		if ( defined $out_tab ) {
+			my $sep = "#";
+			my $ocsv = lib::bih::new() ;
+			my $lm_matrix = undef ;
+			if ( ( $header_choice eq 'yes' ) and ( defined $nbline_header ) and ( $nbline_header > 0 )) {
+				my $header = join("$sep", @$bank_head);
+				my $out_head = "BiH_".$bank_name."_(".$header.")";
+				$lm_matrix = $ocsv->set_lm_matrix_object($out_head, $masses, $col_mzdb, $results, $rt, $rtdb, $bank_head, $sep ) ;
+				$lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ;
+			}
+			elsif ( ( $header_choice eq 'no' ) or ( $nbline_header <= 0 )) {
+				$lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $col_mzdb, $results, $rt, $rtdb, $bank_head, $sep ) ;
+				$lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ;
+			}
+			else {	croak "The number of header line is not identifiable\n" ;	}
+			$ocsv->write_csv_skel(\$out_tab, $lm_matrix) ;
+		}
+		else {	croak "Can't create a tabular output for BiH : your output file is not defined\n" ;	}
+	}
+	elsif (defined $mass) { } ## no csv output for manual masses
+	else {	croak "the input format is not identifiable or your output file is not defined\n" ;	}
+} ## END IF
+else {	croak "Can't create a tabular output for BiH : no result found\n" ;	}
+
+## -------------- Produce Full output ------------------ :
+if (defined $results) {
+	if ( defined $masses_file ) {
+		if ( defined $out_full ) {
+			my $sep = "\t";
+			my $ofull = lib::bih::new() ;
+			if ( ( $header_choice eq 'yes' ) and ( defined $nbline_header ) and ( $nbline_header > 0 )) {
+				$ofull->write_full_excel_like($complete_rows, $sep, $masses, $mz_delta_type, $mz_delta, $col_mzdb, $rt, $rt_delta, $rtdb, $results, $out_full, $nbline_header, $bank_head, "BiH_$bank_name") ;
+			}
+			elsif ( ( $header_choice eq 'no' ) or ( $nbline_header <= 0 )) {
+				$ofull->write_full_excel_like($complete_rows, $sep, $masses, $mz_delta_type, $mz_delta, $col_mzdb, $rt, $rt_delta, $rtdb, $results, $out_full, 0, undef, undef) ;
+			}
+			else {	croak "The number of header line is not identifiable\n" ;	}
+		}
+	}
+	elsif (defined $mass) { } ## no csv output for manual masses
+	else {	croak "the input format is not identifiable or your output file is not defined\n" ;	}
+} ## END IF
+else {	croak "Can't create a full output for BiH : no result found\n" ;	}
+
+
+#====================================================================================
+# Help subroutine called with -h option
+# number of arguments : 0
+# Argument(s)        :
+# Return           : 1
+#====================================================================================
+sub help {
+	print STDERR "
+bank_inhouse
+
+# bank_inhouse is a script to query a in house bank (file) using chemical mass and return a list of common names.
+# Input : mass or list of masses
+# Author : Marion LANDI and Franck Giacomoni (for the Rest part)
+# Email : franck.giacomoni\@clermont.inra.fr
+# Version : 1.1
+# Created : 15/10/2014
+# Updated : 15/12/2015
+USAGE :		 
+		bank_inhouse.pl -masse [mass]
+		 		-tolerance [Delta of mass (Da)] -mode [Ionization type: positive/negative/neutral] 
+		 		-tissues [Restricted to certain tissues] -- optionnal
+		 		-bank_in [file for in personal house bank] -- optionnal
+		 		-outputTab [output file tabular format] -outputView [output file html format]
+				-verbose
+		OR				
+		bank_inhouse.pl -input [path to list of masses file]
+			-nbHeader [nb of lines of headers : 0-n] -colId [Ids colunm number in input file] -colmass [masses col] -colrt [RT col]
+ 			-tolerance [Delta of mass (Da)] -mode [molecular type: positive/negative/neutral]
+ 			-bank_in [file for in house bank]
+ 			-tissues [Restricted to certain tissues] 
+ 			-outputTab [output file tabular format] -outputView [output file html format]
+		 				
+		OR 
+		bank_inhouse.pl	-masse [mass]
+				-rest [get the PeakForest ref db : yes|no]
+				-mz_delta [Delta type for mass (Da or PPM)] -mass_delta [Delta for mass (Da or PPM)] -mode [molecular type: positive/negative/neutral]
+		 		-outputXls [output xls format]
+		 		
+		Others output formats: 		
+		 		-outputJson [output json format]  -outputFull [output format is input+res]
+		";
+	exit(1);
+}
+
+## END of script - M Landi 
+
+__END__
+
+=head1 NAME
+
+ bank_inhouse.pl -- script for
+
+=head1 USAGE
+
+ bank_inhouse.pl -precursors -arg1 [-arg2] 
+ or bank_inhouse.pl -help
+
+=head1 SYNOPSIS
+
+This script manage ... 
+
+=head1 DESCRIPTION
+
+This main program is a ...
+
+=over 4
+
+=item B<function01>
+
+=item B<function02>
+
+=back
+
+=head1 AUTHOR
+
+Marion LANDI 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 : 15 / 10 / 2014
+
+version 2 : 21 / 11 / 2014
+
+=cut