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master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author fgiacomoni
date Wed, 15 Feb 2023 15:57:49 +0000
parents 23970530a518
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2:23970530a518 3:78afd7f439f3
2 2
3 ## script : hr2_manager.pl 3 ## script : hr2_manager.pl
4 ## VERSIONS : 4 ## VERSIONS :
5 # - 01/03/2019 : Fix P issue, permit more flexible atom settings and add requirements for conda auto managing. 5 # - 01/03/2019 : Fix P issue, permit more flexible atom settings and add requirements for conda auto managing.
6 # - 09/12/2022 : Fix "Additional atomes not taken into account" - Ticket issue #7 6 # - 09/12/2022 : Fix "Additional atomes not taken into account" - Ticket issue #7
7 # - 15/02/2023 : New feature - optionnal managing max atom value
7 8
8 #============================================================================= 9 #=============================================================================
9 # Included modules and versions 10 # Included modules and versions
10 #============================================================================= 11 #=============================================================================
11 ## Perl modules 12 ## Perl modules
30 use vars qw(%parametre); 31 use vars qw(%parametre);
31 my $help = undef ; 32 my $help = undef ;
32 my ( $input_file, $line_header, $col_id, $col_mass ) = ( undef, undef, undef, undef ) ; # manage input option file of masses 33 my ( $input_file, $line_header, $col_id, $col_mass ) = ( undef, undef, undef, undef ) ; # manage input option file of masses
33 my ( $mass ) = ( undef ) ; # manage input option masses list 34 my ( $mass ) = ( undef ) ; # manage input option masses list
34 my ( $tolerance, $mode, $charge, $has_golden_rules, $atomes, $atomes_basic ) = ( undef, undef, undef, undef, undef, undef ) ; # manage params 35 my ( $tolerance, $mode, $charge, $has_golden_rules, $atomes, $atomes_basic ) = ( undef, undef, undef, undef, undef, undef ) ; # manage params
36 my ( $C13_max_value, $C12_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value) = (undef, undef,undef,undef,undef,undef,undef,undef,undef,undef,undef,undef) ;
37 my ($customAtomValues) = (undef) ;
35 my ( $output_csv, $output_html ) = ( undef, undef) ; # manage ouputs 38 my ( $output_csv, $output_html ) = ( undef, undef) ; # manage ouputs
36 my $verbose = 2 ; 39 my $verbose = 2 ;
37 40
38 #============================================================================= 41 #=============================================================================
39 # Manage EXCEPTIONS 42 # Manage EXCEPTIONS
48 "mode:s" => \$mode, 51 "mode:s" => \$mode,
49 "charge:i" => \$charge, 52 "charge:i" => \$charge,
50 "regleOr:s" => \$has_golden_rules, 53 "regleOr:s" => \$has_golden_rules,
51 "atomes_basic:s"=> \$atomes_basic, # [basic atoms like CNOHP] 54 "atomes_basic:s"=> \$atomes_basic, # [basic atoms like CNOHP]
52 "atomes_sup:s" => \$atomes, 55 "atomes_sup:s" => \$atomes,
56 #"customAtomValues:s"=> \$customAtomValues,
57
58 "C12_max_value:i" => \$C12_max_value, # OPTIONNAL
59 "C13_max_value:i" => \$C13_max_value,
60 "H_max_value:i" => \$H_max_value,
61 "N_max_value:i" => \$N_max_value,
62 "O_max_value:i" => \$O_max_value,
63 "P_max_value:i" => \$P_max_value,
64 "S_max_value:i" => \$S_max_value,
65 "F_max_value:i" => \$F_max_value,
66 "Cl_max_value:i" => \$Cl_max_value,
67 "K_max_value:i" => \$K_max_value,
68 "Br_max_value:i" => \$Br_max_value,
69 "Na_max_value:i" => \$Na_max_value,
70
53 "output1:s" => \$output_csv, 71 "output1:s" => \$output_csv,
54 "outputView:s" => \$output_html, 72 "outputView:s" => \$output_html,
55 "verbose:i" => \$verbose, 73 "verbose:i" => \$verbose,
56 ) ; 74 ) ;
57 75
61 $help and &help ; 79 $help and &help ;
62 80
63 #============================================================================= 81 #=============================================================================
64 # MAIN SCRIPT 82 # MAIN SCRIPT
65 #============================================================================= 83 #=============================================================================
66 my %atomsConf = () ; 84
67 $atomsConf{'C'} = {'min' => 0, 'max' => 0} ; 85 #print "CUSTOM C12: $C12_max_value\n" if (defined $C12_max_value) ;
68 $atomsConf{ 'H'} = {'min' => 0, 'max' => 0} ; 86 #print "CUSTOM H: $H_max_value if (defined $H_max_value) ;
69 $atomsConf{ 'N'} = {'min' => 0, 'max' => 0} ; 87 #print "CUSTOM N: $N_max_value if (defined $N_max_value) ;
70 $atomsConf{ 'O'} = {'min' => 0, 'max' => 0} ; 88 #print "CUSTOM O: $O_max_value if (defined $O_max_value) ;
71 $atomsConf{ 'P'} = {'min' => 0, 'max' => 0} ; 89 #print "CUSTOM P: $P_max_value if (defined $P_max_value) ;
72 $atomsConf{ 'S'} = {'min' => 0, 'max' => 0} ; 90 #print "CUSTOM S: $S_max_value if (defined $S_max_value) ;
73 $atomsConf{ 'F'} = {'min' => 0, 'max' => 0} ; 91 #print "CUSTOM F: $F_max_value if (defined $F_max_value) ;
74 $atomsConf{ 'L'} = {'min' => 0, 'max' => 0} ; 92 #print "CUSTOM Cl: $Cl_max_value if (defined $Cl_max_value) ;
75 $atomsConf{ 'K'} = {'min' => 0, 'max' => 0} ; 93 #print "CUSTOM K: $K_max_value if (defined $K_max_value) ;
76 $atomsConf{ 'B'} = {'min' => 0, 'max' => 0} ; 94 #print "CUSTOM Br: $Br_max_value if (defined $Br_max_value) ;
77 $atomsConf{ 'A'} = {'min' => 0, 'max' => 0} ; 95 #print "CUSTOM Na: $Na_max_value if (defined $Na_max_value) ;
78 $atomsConf{ '1'} = {'min' => 0, 'max' => 0} ; 96 #print "CUSTOM C13: $C13_max_value if (defined $C13_max_value) ;
79 97
80 ## -------------- Conf file and verbose ------------------------ : 98 ## -------------- Conf file and verbose ------------------------ :
81 my ( $CONF ) = ( undef ) ; ## verbose level is 3 for debugg 99 my ( $CONF ) = ( undef ) ; ## verbose level is 3 for debugg
82 my $time_start = time ; 100 my $time_start = time ;
83 101
102 120
103 ## manage atoms and their ranges 121 ## manage atoms and their ranges
104 #$hr_atoms_list = $ohr->manage_atoms(\$atomes, \$CONF->{'DEFAULT_ATOMS'}) ; ## DEPRECATED 122 #$hr_atoms_list = $ohr->manage_atoms(\$atomes, \$CONF->{'DEFAULT_ATOMS'}) ; ## DEPRECATED
105 123
106 # manage atoms and their ranges with a hash structure 124 # manage atoms and their ranges with a hash structure
107 my $atomsCurrentConf = $ohr->manage_atoms_and_ranges(\%atomsConf, $CONF, $atomes_basic, $atomes) ; 125
108 126 my $AtomsFullConf = $ohr->manageAtomsConf($CONF, $C12_max_value, $C13_max_value, $H_max_value, $N_max_value, $O_max_value, $P_max_value, $S_max_value, $F_max_value, $Cl_max_value, $K_max_value, $Br_max_value, $Na_max_value ) ;
109 #if ( defined $hr_atoms_list ) { 127
110 # ## implements range foreach atom 128 my $atomsCurrentConf = $ohr->manage_atoms_and_ranges($AtomsFullConf, $atomes_basic, $atomes) ;
111 # foreach my $atom ( (split(",", $$hr_atoms_list )) ) {
112 # my $range_max = $CONF->{'DEFAULT_MAX'} ; # manage max value in case of
113 # if ( exists $CONF->{$atom} ) { $range_max = $CONF->{$atom} ; }
114 # my $ref_range = $ohr->manage_atom_and_range(\$atom, \$CONF->{'DEFAULT_MIN'}, \$range_max ) ;
115 # $hr_atoms_and_ranges .= $$ref_range ; ## concat ranges
116 # }
117 #}
118 #else { croak "No atom detected with input params\n" ; }
119 129
120 ## Parsing input file with masses/ids or unik mass : 130 ## Parsing input file with masses/ids or unik mass :
121 ## manage only one mass 131 ## manage only one mass
122 if ( ( defined $mass ) and ( $mass ne "" ) and ( $mass > 0 ) ) { 132 if ( ( defined $mass ) and ( $mass ne "" ) and ( $mass > 0 ) ) {
123 $ids = ['mass_01'] ; 133 $ids = ['mass_01'] ;
153 ## prepare cmd 163 ## prepare cmd
154 foreach my $mz (@{ $masses }) { 164 foreach my $mz (@{ $masses }) {
155 ## computes mass 165 ## computes mass
156 my $ohr_mode = lib::hr->new() ; 166 my $ohr_mode = lib::hr->new() ;
157 my ( $exact_mass ) = $ohr_mode->manage_mode( \$mode, \$charge, \$CONF->{'electron'}, \$CONF->{'proton'}, \$mz ) ; 167 my ( $exact_mass ) = $ohr_mode->manage_mode( \$mode, \$charge, \$CONF->{'electron'}, \$CONF->{'proton'}, \$mz ) ;
158 print "Current MZ send to HR\n" if $verbose == 3 ; 168 print "Current MZ $$exact_mass send to HR\n" if $verbose == 3 ;
159 print Dumper $exact_mass if $verbose == 3 ;
160 ## build exe line 169 ## build exe line
161 my $ohr_exe = lib::hr->new() ; 170 my $ohr_exe = lib::hr->new() ;
162 my $hr_cmd = $ohr_exe->config_hr_exe( \$CONF->{'HR2_EXE'}, \$tolerance, $exact_mass, \$has_golden_rules, \$atomsCurrentConf ) ; 171 my $hr_cmd = $ohr_exe->config_hr_exe( \$CONF->{'HR2_EXE'}, \$tolerance, $exact_mass, \$has_golden_rules, \$atomsCurrentConf ) ;
163 print "$$hr_cmd\n" if $verbose == 3 ; 172 print "\t$$hr_cmd\n" if $verbose == 3 ;
164 push(@{$hr_cmds}, $$hr_cmd) ; 173 push(@{$hr_cmds}, $$hr_cmd) ;
165 } 174 }
166 175
167 ## MultiThreading execution of Hr : 176 ## MultiThreading execution of Hr :
168 my $threads = lib::hr->new() ; 177 my $threads = lib::hr->new() ;
223 232
224 233
225 234
226 ### VERBOSE OUTPUTs 235 ### VERBOSE OUTPUTs
227 if ( $verbose == 3 ) { 236 if ( $verbose == 3 ) {
228 print "-- Conf file contains :\n" ; 237 print "\n\n-- Conf file contains :\n" ;
229 print Dumper $CONF ; 238 print Dumper $CONF ;
230 print "-- Atoms input list :\n" ; 239 print "-- Atoms input list :\n" ;
231 print Dumper $atomes_basic ; 240 print Dumper $atomes_basic ;
232 print "-- Suppl. atoms input list :\n" ; 241 print "-- Suppl. atoms input list :\n" ;
233 print Dumper $atomes ; 242 print Dumper $atomes ;
338 347
339 version 4 : 01/03/2019 348 version 4 : 01/03/2019
340 349
341 version 5 : 09/12/2022 350 version 5 : 09/12/2022
342 351
352 version 6 : 15/02/2023
353
343 =cut 354 =cut