diff hr2_manager.pl @ 0:86296c048e46 draft

Init repository for [hr2]

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hr2_manager.pl	Wed Jun 05 09:40:20 2019 -0400
@@ -0,0 +1,335 @@
+#!perl
+
+## script  : hr2_manager.pl
+## VERSIONS :
+#	- 01/03/2019 : Fix P issue, permit more flexible atom settings and add requirements for conda auto managing.
+
+#=============================================================================
+#                              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 FindBin ; ## Allows you to locate the directory of original perl script
+
+## Dedicate Perl Modules (Home made...)
+use lib $FindBin::Bin ;
+my $binPath = $FindBin::Bin ;
+use lib::hr qw( :ALL ) ;
+## PFEM Perl Modules
+use lib::conf  qw( :ALL ) ;
+use lib::csv  qw( :ALL ) ;
+
+## Initialized values
+use vars qw(%parametre);
+my $help = undef ; 
+my ( $input_file, $line_header, $col_id, $col_mass ) = ( undef, undef, undef, undef ) ; # manage input option file of masses
+my ( $mass ) = ( undef ) ; # manage input option masses list
+my ( $tolerance, $mode, $charge, $has_golden_rules, $atomes, $atomes_basic ) = ( undef, undef, undef, undef, undef, undef ) ; # manage params
+my ( $output_csv, $output_html ) = ( undef, undef) ; # manage ouputs
+my $verbose = 2 ;
+
+#=============================================================================
+#                                Manage EXCEPTIONS
+#=============================================================================
+&GetOptions ( 	"h"     		=> 	\$help,       # HELP
+				"input:s"		=>	\$input_file,
+				"colId:i"		=>	\$col_id,
+				"nbHeader:i"	=>	\$line_header,
+				"colmass:i"		=>	\$col_mass,
+				"masse:s"		=>	\$mass,
+				"tolerance:f"	=>	\$tolerance,
+				"mode:s"		=>	\$mode,
+				"charge:i"		=>	\$charge,
+				"regleOr:s"		=>	\$has_golden_rules,
+				"atomes:s"		=>	\$atomes_basic, # [basic atoms like CNOHP]
+				"atomessup:s"	=>	\$atomes,
+				"output1:s"		=>	\$output_csv,
+				"outputView:s"	=>	\$output_html,
+				"verbose:i"		=> 	\$verbose,
+            ) ;
+         
+#=============================================================================
+#                                EXCEPTIONS
+#=============================================================================
+$help and &help ;
+
+#=============================================================================
+#                                MAIN SCRIPT
+#=============================================================================
+my %atomsConf = () ;
+$atomsConf{'C'} = {'min' => 0, 'max' =>  0} ;
+$atomsConf{	'H'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'N'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'O'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'P'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'S'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'F'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'L'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'K'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'B'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'A'} = {'min' => 0, 'max' => 0} ;
+$atomsConf{	'1'} = {'min' => 0, 'max' => 0} ;
+
+## -------------- Conf file and verbose ------------------------ :
+my ( $CONF ) = ( undef ) ; ## verbose level is 3 for debugg
+my $time_start = time ;
+
+foreach my $conf ( <$binPath/*.cfg> ) {
+	my $oConf = lib::conf::new() ;
+	$CONF = $oConf->as_conf($conf) ;
+}
+## --------------- Global parameters ---------------- :
+my ( $ids, $masses, $hr_cmds, $results, $parsed_results ) = ( undef, undef, undef, undef, undef ) ;
+my $complete_rows = undef ;
+my ($hr_atoms_list, $hr_atoms_and_ranges, $set_tol, ) = (undef, undef, undef, ) ;
+
+## Check and manage params
+my $ohr = lib::hr->new() ;
+
+## set tolerance
+$set_tol = $ohr->manage_tolerance( \$tolerance, \$CONF->{'tolerance'} ) ;
+
+## check HR exe envt :
+my $hr_check = $ohr->check_hr_exe(\$CONF->{'HR2_EXE'}, \$CONF->{'HR2_VERSION'}) ;
+if (!defined $hr_check ) { croak "No hr exe available (wrong path) or wrong version will be used  -- end of script\n" ; }
+
+## manage atoms and their ranges
+#$hr_atoms_list = $ohr->manage_atoms(\$atomes, \$CONF->{'DEFAULT_ATOMS'}) ; ## DEPRECATED
+
+# manage atoms and their ranges with a hash structure
+my $atomsCurrentConf = $ohr->manage_atoms_and_ranges(\%atomsConf, $CONF, $atomes_basic, $atomes) ;
+
+#if ( defined $hr_atoms_list ) {
+#	## implements range foreach atom
+#	foreach my $atom ( (split(",", $$hr_atoms_list )) ) {
+#		my $range_max = $CONF->{'DEFAULT_MAX'} ; # manage max value in case of
+#		if ( exists $CONF->{$atom} ) 	{ $range_max = $CONF->{$atom} ; }
+#		my $ref_range = $ohr->manage_atom_and_range(\$atom, \$CONF->{'DEFAULT_MIN'}, \$range_max ) ;
+#		$hr_atoms_and_ranges .= $$ref_range ; ## concat ranges
+#	}
+#}
+#else { 	croak "No atom detected with input params\n" ; }
+
+## Parsing input file with masses/ids or unik mass :
+## manage only one mass
+if ( ( defined $mass ) and ( $mass ne "" ) and ( $mass > 0 ) ) {
+	$ids = ['mass_01'] ;
+	$masses = [$mass] ;
+	
+} ## END IF
+## manage csv file containing list of masses
+elsif ( ( defined $input_file ) and ( $input_file ne "" ) and ( -e $input_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, \$input_file) ;
+	
+	## parse csv ids and masses
+	my $is_header = undef ;
+	my $ocsv = lib::csv->new() ;
+	my $csv = $ocsv->get_csv_object( "\t" ) ;
+	if ( ( defined $line_header ) and ( $line_header > 0 ) ) { $is_header = 'yes' ;	}		else{ $is_header = 'no' ; }
+	$masses = $ocsv->get_value_from_csv_multi_header( $csv, $input_file, $col_mass, $is_header, $line_header ) ; ## retrieve mz values on csv
+	$ids = $ocsv->get_value_from_csv_multi_header( $csv, $input_file, $col_id, $is_header, $line_header ) ; ## retrieve ids values on csv
+	
+}
+else {
+	croak "Can't work with HR2 : missing input file or mass (list of masses, ids)\n" ;
+} ## end ELSE
+
+## check using golden rules
+if ( $has_golden_rules eq 'NO') { $has_golden_rules = undef ; }
+
+## ---------------- launch queries -------------------- :
+
+## prepare cmd
+foreach my $mz (@{ $masses }) {
+	## computes mass
+	my $ohr_mode = lib::hr->new() ;
+	my ( $exact_mass ) = $ohr_mode->manage_mode( \$mode, \$charge, \$CONF->{'electron'}, \$CONF->{'proton'}, \$mz ) ;
+	print "Current MZ send to HR\n"  if $verbose == 3 ;
+	print Dumper $exact_mass if $verbose == 3 ;
+	## build exe line
+	my $ohr_exe = lib::hr->new() ;
+	my $hr_cmd = $ohr_exe->config_hr_exe( \$CONF->{'HR2_EXE'}, \$tolerance, $exact_mass, \$has_golden_rules, \$atomsCurrentConf ) ;
+	print "$hr_cmd\n" if $verbose == 3 ;
+	push(@{$hr_cmds}, $$hr_cmd) ;
+}
+
+## MultiThreading execution of Hr :
+my $threads = lib::hr->new() ;
+my $hr_object = lib::hr->new() ;
+if ( $hr_object->can('hr_exe') ) {
+	my $method = $hr_object->can('hr_exe') ;
+	$results = $threads->threading_hr_exe( $method, $hr_cmds) ;
+
+}
+
+## MultiThreading parsing of Hr outputs :
+my $hrres_object = lib::hr->new() ;
+if ( $hrres_object->can('hr_out_parser') ) {
+	my $method = $hr_object->can('hr_out_parser') ;
+	if ( defined $results ) { 	$parsed_results = $threads->threading_hr_exe( $method, $results ) ; }
+}
+
+## -------------- Produce HTML/CSV output ------------------ :
+my $search_condition = 'Mode used: '.$mode.' / Charge: +'.$charge.' / Mass tolerance: '.$$set_tol.' / Composition: '.$atomsCurrentConf ;
+## Uses N mz and theirs entries per page (see config file).
+# how many pages you need with your input mz list?
+my $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} )  ;
+
+if ( ( defined $output_html ) and ( defined $parsed_results ) ) {	
+	my $oHtml = lib::hr::new() ;
+	my ($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, $parsed_results ) ;
+	($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $parsed_results) ;
+	my $html_file = $binPath.'/'.$CONF->{'HTML_TEMPLATE'} ;
+	my $output = $oHtml->write_html_skel(\$output_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $html_file, $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" ;
+}
+
+if ( ( defined $output_csv ) and ( defined $parsed_results ) ) {
+	# produce a csv based on METLIN format
+	my $ocsv = lib::hr::new() ;
+	if (defined $input_file) {
+		my $lm_matrix = undef ;
+		if ( ( defined $line_header ) and ( $line_header == 1 ) ) { $lm_matrix = $ocsv->set_hr_matrix_object('hr2', $masses, $parsed_results ) ; }
+		elsif ( ( defined $line_header ) and ( $line_header == 0 ) ) { $lm_matrix = $ocsv->set_hr_matrix_object(undef, $masses, $parsed_results ) ; }
+		$lm_matrix = $ocsv->add_hr_matrix_to_input_matrix($complete_rows, $lm_matrix) ;
+		$ocsv->write_csv_skel(\$output_csv, $lm_matrix) ;
+	}
+	elsif (defined $mass) {
+		$ocsv->write_csv_one_mass($masses, $ids, $parsed_results, $output_csv) ;
+	}
+} ## END IF
+else {
+#	croak "Can't create a tabular output for HR2 : no result found or your output file is not defined\n" ;
+}
+
+
+
+### VERBOSE OUTPUTs
+if ( $verbose == 3 ) {
+	print "-- Conf file contains :\n" ;
+	print Dumper $CONF ;
+	print "-- Atoms input list :\n" ;
+	print Dumper $atomes_basic ;
+	print "-- Suppl. atoms input list :\n" ;
+	print Dumper $atomes ;
+	print "-- HR envt ready  :\n" ;
+	print Dumper $hr_check ;
+	print "-- Atoms and ranges :\n" ;
+	print Dumper $atomsCurrentConf ;
+	print "-- Tolerance :\n" ;
+	print Dumper $set_tol ;
+	print "-- Complete input file :\n" ;
+	print Dumper $complete_rows ;
+	print "-- Inputs initiales masses :\n" ;
+	print Dumper $masses ;
+	print "-- Inputs initiales ids :\n" ;
+	print Dumper $ids ;
+	print "-- Hr_Cmds :\n" ;
+	print Dumper $hr_cmds ;
+	print "-- Hr_Results :\n" ;
+#	print Dumper $results ;
+	print "-- Hr_parsed Results :\n" ;
+	print Dumper $parsed_results ;
+	
+	my $nb_results = scalar (@{$results}) ;
+	print "-- Hr_Results return  : $nb_results\n" ;
+}
+
+my $time_end = time ;
+my $seconds = $time_end-$time_start ;
+print "\n------  Time used in threaded mode by 6 : $seconds seconds --------\n\n" ;
+
+
+
+
+
+
+#====================================================================================
+# Help subroutine called with -h option
+# number of arguments : 0
+# Argument(s)        :
+# Return           : 1
+#====================================================================================
+sub help {
+	print STDERR "
+hr2_manager.pl
+
+# hr2_manager is a script to elucide chemical formula by their accurate masses. The HiRes program is integrate in this package
+# Input : a accurate mass or a file of masses
+# Author : Franck Giacomoni and Marion Landi
+# Email : fgiacomoni\@clermont.inra.fr or mlandi\@clermont.inra.fr
+# Version : 1.1
+# Created : 01/12/2011
+# Last Update : 09032014
+USAGE :		 
+		hr2_manager.pl -h or
+		hr2_manager.pl -input [cvs file of masses] -colId [int] -colmass [int] -nbHeader [int] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
+		hr2_manager.pl -masse [double] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
+	" ;
+	exit(1);
+}
+
+## END of script - F Giacomoni 
+
+__END__
+
+=head1 NAME
+
+ hr2_manager.pl -- script for launch / manage hr2 binary
+
+=head1 USAGE
+
+ hr2_manager.pl -h or
+ hr2_manager.pl -input [cvs file of masses] -colId [int] -colmass [int] -nbHeader [int] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
+ hr2_manager.pl -masse [double] -tolerance [float] -mode [positive, neutral or negative] -charge [int] -regleOr [yes or no] -atome [P, S, F, Cl, K, B, A, 1 ] -output1 [csv file] -outputView [html file]
+
+=head1 SYNOPSIS
+
+This script manages hr2 binary which elucids raw formula with exact masses.
+
+=head1 DESCRIPTION
+
+This main program is a module to elucidate chemical formula with HiRes program. Source is available on Fiehn lab web.
+
+=over 4
+
+=item B<function01>
+
+=item B<function02>
+
+=back
+
+=head1 AUTHOR
+
+Franck Giacomoni E<lt>[e-mail]<gt>
+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 : 18/07/2012
+
+version 2 : 02/10/2013
+
+version 3 : 20/02/2014
+
+version 4 : 01/03/2019
+
+=cut
\ No newline at end of file