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date Thu, 04 Oct 2018 10:37:14 -0400
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1 #!perl
2
3 ## script : bank_inhouse.pl
4 #=============================================================================
5 # Included modules and versions
6 #=============================================================================
7 ## Perl modules
8 use strict ;
9 use warnings ;
10 use Carp qw (cluck croak carp) ;
11
12 use Data::Dumper ;
13 use Getopt::Long ;
14 use POSIX ;
15 use List::Util qw( min max );
16 use FindBin ; ## Allows you to locate the directory of original perl script
17
18 ## Specific Modules
19 use lib $FindBin::Bin ;
20 my $binPath = $FindBin::Bin ;
21 use lib::bih qw( :ALL ) ;
22
23 ## PFEM Perl Modules
24 use lib::conf qw( :ALL ) ;
25 use lib::csv qw( :ALL ) ;
26
27 ## Initialized values
28 my ( $help ) = ( undef ) ;
29 my ( $mass ) = ( undef ) ;
30 my ( $masses_file, $nbline_header, $col_mass ) = ( undef, undef, undef ) ;
31 my ( $col_rt, $manual_rt, $rt_delta, $mz_delta_type, $mz_delta, $rtdb ) = ( undef, undef, undef, undef, undef, undef ) ;
32 my ( $mode, $tissues, $bank_in, $bank_name, $col_mzdb) = ( undef, undef, undef, undef, undef ) ;
33 my ( $out_tab, $out_html, $out_xls, $out_json, $out_full ) = ( undef, undef, undef, undef, undef ) ;
34 my ($rest_mode) = ('no') ;
35
36 my ( $verbose ) = ( 2 ) ; ## verbose level is 3 for debugg
37
38 #=============================================================================
39 # Manage EXCEPTIONS
40 #=============================================================================
41
42 &GetOptions ( "h" => \$help, # HELP
43 "masse:s" => \$mass, ## option : one masse
44 "input:s" => \$masses_file, ## option : path to the input
45 "rest:s" => \$rest_mode, ## option : allow uses of peakforest rest service
46 "nbheader:i" => \$nbline_header, ## numbre of header line present in file
47 "colrt:i" => \$col_rt, ## Column retention time for retrieve formula/masses list in tabular file
48 "rt:s" => \$manual_rt, ## Retention time for manual masses list
49 "rt_delta:f" => \$rt_delta, ## Delta for retention time
50 "colmass:i" => \$col_mass, ## Column id for retrieve formula list in tabular file
51 "mz_delta:s" => \$mz_delta_type, ## Delta type for masses
52 "mass_delta:f" => \$mz_delta, ## Delta for masses
53 "mode:s" => \$mode, ## Molecular species (positive/negative/neutral)
54 "tissues:s" => \$tissues, ## Restricted to certain characterization and localization (blood/plasma/urine/peptide)
55 "bank_in:s" => \$bank_in, ## option : path to a personal data bank
56 "bank_name:s" => \$bank_name, ## option : name of the bank
57 "mzdb:i" => \$col_mzdb, ## Column number in which is the masses of the personal data bank
58 "rtdb:i" => \$rtdb, ## Column number in which is the retention time of the personal data bank
59 "outputJson:s" => \$out_json, ## option : path to the ouput (results)
60 "outputXls:s" => \$out_xls, ## option : path to the ouput (tabular : results )
61 "outputTab:s" => \$out_tab, ## path to the ouput (tabular : input+results (1 col) )
62 "outputView:s" => \$out_html, ## option : path to the results view (output2)
63 "outputFull:s" => \$out_full, ## path to the ouput (tabular : input+results (x col) )
64 ) ;
65
66 #=============================================================================
67 # EXCEPTIONS
68 #=============================================================================
69 ## if you put the option -help or -h function help is started
70 if ( defined $help ) { &help() ; }
71
72 #=============================================================================
73 # MAIN SCRIPT
74 #=============================================================================
75
76
77 print "The bank_inhouse program is launched as:\n";
78 print "./bank_inhouse.pl " ;
79 print "--h " if (defined $help) ;
80 print "--masse $mass " if (defined $mass) ;
81 print "--input $masses_file " if (defined $masses_file) ;
82 print "--rest $rest_mode " if (defined $rest_mode) ;
83 print "--nbheader $nbline_header " if (defined $nbline_header) ;
84 print "--colrt $col_rt " if (defined $col_rt) ;
85 print "--rt $manual_rt " if (defined $manual_rt) ;
86 print "--colmass $col_mass " if (defined $col_mass) ;
87 print "--mz_delta $mz_delta_type " if (defined $mz_delta_type) ;
88 print "--mass_delta $mz_delta " if (defined $mz_delta) ;
89 print "--mode $mode " if (defined $mode) ;
90 print "--tissues $tissues " if (defined $tissues) ;
91 print "--bank_in $bank_in " if (defined $bank_in) ;
92 print "--bank_name $bank_name " if (defined $bank_name) ;
93 print "--mzdb $col_mzdb " if (defined $col_mzdb) ;
94 print "--rtdb $rtdb " if (defined $rtdb) ;
95 print "--outputJson $out_json " if (defined $out_json) ;
96 print "--outputXls $out_xls " if (defined $out_xls) ;
97 print "--outputTab $out_tab " if (defined $out_tab) ;
98 print "--outputView $out_html " if (defined $out_html) ;
99 print "--outputFull $out_full " if (defined $out_full) ;
100 print "\n" ;
101
102
103
104 ## -------------- Conf file ------------------------ :
105 my ( $CONF, $PF_CONF ) = ( undef, undef ) ;
106 foreach my $conf ( <$binPath/*.cfg> ) {
107 my $oConf = lib::conf::new() ;
108 $CONF = $oConf->as_conf($conf) ;
109 }
110
111 ## PForest dedicated conf
112 if ((defined $rest_mode ) and ( $rest_mode eq "yes" )) {
113 foreach my $ini ( <$binPath/*.ini> ) {
114 my $oConf = lib::conf::new() ;
115 $PF_CONF = $oConf->as_conf($ini) ;
116 }
117 }
118
119 ## --------------- Global parameters ---------------- :
120 my ( $masses, $rt, $results, $header_choice ) = ( undef, undef, undef, undef, undef ) ; ##############
121 my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ;
122
123 my $oBih = lib::bih::new() ;
124
125 ## --------------- retrieve input data -------------- :
126
127 ## manage manual mass(es)
128 if ( ( defined $mass ) and ( $mass ne "" ) ) {
129 $mass =~ tr/,/./ ;
130 @$masses = split(' ', $mass);
131 if ( ( defined $manual_rt ) and ( $manual_rt ne "" ) ) {
132 $manual_rt =~ tr/,/./ ;
133 @$rt = split(' ', $manual_rt) ;
134 if ( $#$rt != $#$masses) { croak "You have not given the same number of masses and retention time\n" ; }
135 }
136 } ## END IF
137
138 ## manage csv file containing list of masses
139 elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) {
140 ## parse all csv for later : output csv build
141 my $ocsv_input = lib::csv->new() ;
142 my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
143 $complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ;
144
145 ## parse csv ids and masses
146 my $ocsv = lib::csv->new() ;
147 my $csv = $ocsv->get_csv_object( "\t" ) ;
148 if ( ( defined $nbline_header ) and ( $nbline_header > 0 ) ) { $header_choice = 'yes' ; } else{ $header_choice = 'no' ; }
149 $masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv
150 if ( ( defined $col_rt ) and ( $col_rt ne "" ) ) {
151 $rt = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_rt, $header_choice, $nbline_header ) ; ## retrieve rt values on csv
152 }
153 }
154
155 # --------------- retrieve personal data bank input -------------- :
156
157 my ($complete_bank, $bank_head) = (undef, undef) ;
158
159 ## check up $bank_in and parse
160 if ( ( defined $bank_in ) and ( $bank_in ne '' ) and ( -e $bank_in ) and ( defined $col_mzdb ) and ( $col_mzdb ne '' ) ) {
161 ## parse csv bank_in
162 my $ocsv_input = lib::csv->new() ;
163 my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
164 ($complete_bank, $bank_head)= $oBih->parse_bank_interest($complete_csv, \$bank_in, $col_mzdb-1) ;
165 }
166 ## manage rest service of PeakForest and set $masses and $rt with given databases
167 elsif ( ( defined $rest_mode ) and ( $rest_mode eq "yes" ) ) {
168 $bank_name = "PeakForest";
169 if ( ( $PF_CONF->{PF_GLOBAL_TOKEN} ne "" ) and ( $PF_CONF->{PF_WS_URL} ne "" ) ) {
170 ## init
171 my $opfws = lib::bih::new() ;
172 ## get min and max values of user query
173 my ($min, $max) = (0, 0) ;
174
175 if ( ( defined $masses ) and ( scalar (@{$masses}) > 0 ) ) {
176 $min = min @{$masses} ;
177 $max = max @{$masses} ;
178 # print Dumper $masses ;
179 ## TODO: adjust min and max with delta
180 my ( $min_delta, undef ) = $opfws->mz_delta_conversion(\$min, \$mz_delta_type, \$mz_delta) ;
181 my ( undef, $max_delta ) = $opfws->mz_delta_conversion(\$max, \$mz_delta_type, \$mz_delta) ;
182
183 ## get clean range database json from PForest WS :
184 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) ;
185 if (defined $pf_json) {
186 ($complete_bank, $bank_head) = $opfws->map_pfjson_bankobject($pf_json) ;
187 }
188 } ## End IF
189 else {
190 croak "Fatal error : your mass list is empty\n" ;
191 }
192 } ## End IF PForest param
193 else { croak "Can't work : missing a PForest REST paramater\n" ; }
194 } ## End ELSIF PForest
195 elsif ( ( defined $CONF->{'INHOUSE_BANK'} ) and ( $CONF->{'INHOUSE_BANK'} ne '' ) ) {
196 $col_mzdb = 4;
197 $bank_name = "internal_bank";
198 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" ; }
199 my $html_file = $binPath.'/'.$CONF->{'INHOUSE_BANK'} ;
200 if ( -e $html_file ) {
201 ## parse all csv for later : output csv build
202 my $ocsv_input = lib::csv->new() ;
203 my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
204 ($complete_bank, $bank_head)= $oBih->parse_bank_interest($complete_csv, \$html_file, $col_mzdb-1) ;
205 }
206 else { croak "Can't work : no local inhouse bank name '$html_file'\n" ; }
207 }
208 else { croak "Can't work : missing an inhouse bank\n" ; }
209
210 ## ---------------- launch queries -------------------- :
211
212 my $ionization = undef ;
213 my $characterization = undef ;
214 my $valH = undef ;
215 my $bank = undef ;
216 my $search_condition = undef ;
217
218 #($valH, $ionization)= $oBih->manage_mode($mode, $CONF->{'PROTON_MZ'}, $CONF->{'ELECTRON_MZ'}) ;
219
220 ######### Manage Tissues ##############################################################################
221 #if ( ( !defined $tissues ) or ( $tissues eq '' ) or ( $tissues eq 'none' ) ) {
222 # $characterization = ['None'];
223 #} else { @{$characterization} = split(",", $tissues); }
224 ######### End #########################################################################################
225
226 #if ( (@$ionization = (['None'])) and (@$characterization = (['None']))) { $bank = $complete_bank; }
227 #else { $bank = FILTER LA BANK; }
228 $bank = $complete_bank;
229 $valH = 0 ;
230
231 #if ( ( defined $mz_delta ) and ( $mz_delta > 0 ) and ( defined $ionization ) and ( defined $characterization ) and ( defined $masses ) and ( defined $ids ) and ( defined $bank ) ) {
232 # $search_condition = "Search params : Molecular specie = $mode / delta = $mz_delta / characterization and localization = $tissues \n bank file = $bank_in" ;
233
234 if ( ( defined $mz_delta ) and ( $mz_delta >= 0 ) and ( defined $masses ) and ( defined $bank ) ) {
235 ## prepare masses list and execute query
236 $results = [] ;
237 if ($mz_delta != 0){
238 my @sort_masses_bank = sort { $a <=> $b } keys(%$bank);
239
240 my $compt_masses = 0;
241 foreach my $mz (@$masses) {
242 $compt_masses++;
243 my ($MZmessage) = $oBih->check_interval($mz, 0, 10000) ;
244 if ( $MZmessage eq 'OK' ){
245 my ( $min, $max ) = $oBih->mz_delta_conversion(\$mz, \$mz_delta_type, \$mz_delta) ;
246
247 my ($marj_inf) = $oBih->dichotomi_search(\@sort_masses_bank, $min) ;
248 my ($marj_sup) = $oBih->dichotomi_search(\@sort_masses_bank, $max) ;
249
250 my $result = [];
251 if($$marj_inf != $$marj_sup){
252 if ($$marj_inf == -1){ $$marj_inf=0; }
253 for (my $i=$$marj_inf; $i<$$marj_sup; $i++){
254 my $bank_tmp = $$bank{$sort_masses_bank[$i]};
255 if ( ( defined $rt ) and ( $rt ne "" ) ) {
256 my ($RTmessage) = $oBih->check_interval($$rt[$compt_masses-1], 0, 60) ;
257 if ( $RTmessage eq 'OK' ){
258 my $bank_rt = [];
259 for(my $nb_rt=0; $nb_rt<=$#$bank_tmp; $nb_rt++){
260 my ($RTbank) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], 0, 60) ;
261 my ($RTsearch) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], $$rt[$compt_masses-1]-$rt_delta, $$rt[$compt_masses-1]+$rt_delta) ;
262 if ( ($RTbank eq 'OK') and ($RTsearch eq 'OK') ){
263 push (@$result, $bank_tmp->[$nb_rt]) ;
264 }
265 elsif ($RTbank ne 'OK'){ croak "At least one retention time in bank is not valid : $RTbank\n" ; }
266 }
267 }
268 else { croak "The $compt_masses th analyzed retention time : $RTmessage\n" ; }
269 }
270 else { push (@$result, @$bank_tmp) ; }
271 }
272 }
273 else{ $result = []; }
274 push (@$results, [@$result]) ;
275 }
276 else { croak "The $compt_masses th value : $MZmessage\n" ; }
277 print Dumper $results if ($verbose>2) ;
278 } ## End FOREACH MZ queried
279 } ## End IF
280 else{
281 my $result = [];
282 my $compt_masses = 0;
283 foreach my $mz (@$masses) {
284 $compt_masses++;
285 my ($MZmessage) = $oBih->check_interval($mz, 0, 10000) ;
286 if ( $MZmessage eq 'OK' ){
287 if ($$bank{$mz}){
288 my $bank_tmp = $$bank{$mz};
289 if ( ( defined $rt ) and ( $rt ne "" ) ) {
290 my ($RTmessage) = $oBih->check_interval($$rt[$compt_masses-1], 0, 60) ;
291 if ( $RTmessage eq 'OK' ){my $bank_rt = [];
292 for(my $nb_rt=0; $nb_rt<=$#$bank_tmp; $nb_rt++){
293 my ($RTbank) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], 0, 60) ;
294 my ($RTsearch) = $oBih->check_interval($bank_tmp->[$nb_rt]->[$rtdb-1], $$rt[$compt_masses-1]-$rt_delta, $$rt[$compt_masses-1]+$rt_delta) ;
295 if ( ($RTbank eq 'OK') and ($RTsearch eq 'OK') ){
296 push (@$bank_rt, $bank_tmp->[$nb_rt]) ;
297 }
298 elsif ($RTbank ne 'OK'){ croak "At least one retention time in bank is not valid : $RTbank\n" ; }
299 }
300 if ($#$bank_rt>=0){ ## If there is at least one result
301 push (@$result, $bank_rt) ;
302 } ## else $bank_rt = [] as defined
303 }
304 else { croak "The $compt_masses th analyzed retention time : $RTmessage\n" ; }
305 }
306 else { push (@$result, [$bank_tmp]) ; }
307 }
308 else { push (@$result, [] ) ; }
309 }
310 else { croak "The $compt_masses th mass : $MZmessage\n" ; }
311 }
312 $results = [@$results, @$result] ;
313 }
314 }
315 else {
316 croak "Can't work : missing paramaters (list of ids, masses, delta, ionization, characterization or inhouse_bank)\n" ;
317 } ## end ELSE
318
319
320 if ( ( defined $rt ) and ( $rt ne "" ) ) { unshift (@$bank_head, ("DELTA_mass(".$mz_delta.$mz_delta_type.")", "MASS_Result", "DELTA_RT(".$rt_delta.")", "RT_Result")) ; }
321 else { unshift (@$bank_head, ("DELTA_mass(".$mz_delta.$mz_delta_type.")", "MASS_Result")) ; }
322
323
324 ## -------------- Produce JSON output ------------------ :
325 if ( ( defined $out_json ) and ( defined $results ) ) {
326 open(JSON, '>:utf8', "$out_json") or die "Cant' create the json file\n" ;
327 print JSON Dumper $results;
328 close(JSON) ;
329 } ## END IF
330 else {
331 #croak "Can't create a json output for Massbank : no result found or your output file is not defined\n" ;
332 }
333
334 ## -------------- Produce HTML output ------------------ :
335
336 #if ( ( defined $out_html ) and ( defined $results ) ) {
337 # ## Uses N mz and theirs entries per page (see config file).
338 # # how many pages you need with your input mz list?
339 # $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
340 #
341 # my $oHtml = lib::bih::new() ;
342 # my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
343 # ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
344 # ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
345 # print Dumper $tbody_object;exit;
346 # 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'}) ;
347 #
348 #} ## END IF
349 #else { croak "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ; }
350
351 ## -------------- Produce XLS like output ------------------ :
352 if ( ( defined $out_xls ) and ( defined $results ) ) {
353 my $oxls = lib::bih::new() ;
354 $oxls->write_excel_like_mass($masses, $mz_delta_type, $mz_delta, $col_mzdb, $rt, $rt_delta, $rtdb, $results, $out_xls, $bank_head) ;
355 } ## END IF
356 else { croak "Can't create a tabular output for BiH (like xls): no result found or your output file is not defined\n" ; }
357
358 ## -------------- Produce CSV output ------------------ :
359 if (defined $results) {
360 if ( defined $masses_file ) { # produce a csv based on METLIN format
361 if ( defined $out_tab ) {
362 my $sep = "#";
363 my $ocsv = lib::bih::new() ;
364 my $lm_matrix = undef ;
365 if ( ( $header_choice eq 'yes' ) and ( defined $nbline_header ) and ( $nbline_header > 0 )) {
366 my $header = join("$sep", @$bank_head);
367 my $out_head = "BiH_".$bank_name."_(".$header.")";
368 $lm_matrix = $ocsv->set_lm_matrix_object($out_head, $masses, $col_mzdb, $results, $rt, $rtdb, $bank_head, $sep ) ;
369 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ;
370 }
371 elsif ( ( $header_choice eq 'no' ) or ( $nbline_header <= 0 )) {
372 $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $col_mzdb, $results, $rt, $rtdb, $bank_head, $sep ) ;
373 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ;
374 }
375 else { croak "The number of header line is not identifiable\n" ; }
376 $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ;
377 }
378 else { croak "Can't create a tabular output for BiH : your output file is not defined\n" ; }
379 }
380 elsif (defined $mass) { } ## no csv output for manual masses
381 else { croak "the input format is not identifiable or your output file is not defined\n" ; }
382 } ## END IF
383 else { croak "Can't create a tabular output for BiH : no result found\n" ; }
384
385 ## -------------- Produce Full output ------------------ :
386 if (defined $results) {
387 if ( defined $masses_file ) {
388 if ( defined $out_full ) {
389 my $sep = "\t";
390 my $ofull = lib::bih::new() ;
391 if ( ( $header_choice eq 'yes' ) and ( defined $nbline_header ) and ( $nbline_header > 0 )) {
392 $ofull->write_full_excel_like($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") ;
393 }
394 elsif ( ( $header_choice eq 'no' ) or ( $nbline_header <= 0 )) {
395 $ofull->write_full_excel_like($complete_rows, $sep, $masses, $mz_delta_type, $mz_delta, $col_mzdb, $rt, $rt_delta, $rtdb, $results, $out_full, 0, undef, undef) ;
396 }
397 else { croak "The number of header line is not identifiable\n" ; }
398 }
399 }
400 elsif (defined $mass) { } ## no csv output for manual masses
401 else { croak "the input format is not identifiable or your output file is not defined\n" ; }
402 } ## END IF
403 else { croak "Can't create a full output for BiH : no result found\n" ; }
404
405
406 #====================================================================================
407 # Help subroutine called with -h option
408 # number of arguments : 0
409 # Argument(s) :
410 # Return : 1
411 #====================================================================================
412 sub help {
413 print STDERR "
414 bank_inhouse
415
416 # bank_inhouse is a script to query a in house bank (file) using chemical mass and return a list of common names.
417 # Input : mass or list of masses
418 # Author : Marion LANDI and Franck Giacomoni (for the Rest part)
419 # Email : franck.giacomoni\@clermont.inra.fr
420 # Version : 1.1
421 # Created : 15/10/2014
422 # Updated : 15/12/2015
423 USAGE :
424 bank_inhouse.pl -masse [mass]
425 -tolerance [Delta of mass (Da)] -mode [Ionization type: positive/negative/neutral]
426 -tissues [Restricted to certain tissues] -- optionnal
427 -bank_in [file for in personal house bank] -- optionnal
428 -outputTab [output file tabular format] -outputView [output file html format]
429 -verbose
430 OR
431 bank_inhouse.pl -input [path to list of masses file]
432 -nbHeader [nb of lines of headers : 0-n] -colId [Ids colunm number in input file] -colmass [masses col] -colrt [RT col]
433 -tolerance [Delta of mass (Da)] -mode [molecular type: positive/negative/neutral]
434 -bank_in [file for in house bank]
435 -tissues [Restricted to certain tissues]
436 -outputTab [output file tabular format] -outputView [output file html format]
437
438 OR
439 bank_inhouse.pl -masse [mass]
440 -rest [get the PeakForest ref db : yes|no]
441 -mz_delta [Delta type for mass (Da or PPM)] -mass_delta [Delta for mass (Da or PPM)] -mode [molecular type: positive/negative/neutral]
442 -outputXls [output xls format]
443
444 Others output formats:
445 -outputJson [output json format] -outputFull [output format is input+res]
446 ";
447 exit(1);
448 }
449
450 ## END of script - M Landi
451
452 __END__
453
454 =head1 NAME
455
456 bank_inhouse.pl -- script for
457
458 =head1 USAGE
459
460 bank_inhouse.pl -precursors -arg1 [-arg2]
461 or bank_inhouse.pl -help
462
463 =head1 SYNOPSIS
464
465 This script manage ...
466
467 =head1 DESCRIPTION
468
469 This main program is a ...
470
471 =over 4
472
473 =item B<function01>
474
475 =item B<function02>
476
477 =back
478
479 =head1 AUTHOR
480
481 Marion LANDI E<lt>marion.landi@clermont.inra.frE<gt>
482
483 =head1 LICENSE
484
485 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
486
487 =head1 VERSION
488
489 version 1 : 15 / 10 / 2014
490
491 version 2 : 21 / 11 / 2014
492
493 =cut