Mercurial > repos > fgiacomoni > hmdb_ms_search
diff hmdb/wsdl_hmdb.pl @ 0:9583f9772198 draft
Init and uploaded
author | fgiacomoni |
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date | Thu, 28 Jan 2016 10:52:26 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hmdb/wsdl_hmdb.pl Thu Jan 28 10:52:26 2016 -0500 @@ -0,0 +1,265 @@ +#!perl + +## script : wsdl_hmdb.pl +#============================================================================= +# Included modules and versions +#============================================================================= +## Perl modules +use strict ; +use warnings ; +use Carp qw (cluck croak carp) ; + +use Data::Dumper ; +use Getopt::Long ; +use Text::CSV ; +use POSIX ; +use FindBin ; ## Permet de localisez le repertoire du script perl d'origine + +## Specific Modules (Home made...) +use lib $FindBin::Bin ; +my $binPath = $FindBin::Bin ; +use lib::hmdb 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, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ; +my ( $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef ) ; + + +#============================================================================= +# Manage EXCEPTIONS +#============================================================================= + +&GetOptions ( "h" => \$help, # HELP + "mass:s" => \$mass, ## option : one masse + "masses:s" => \$masses_file, ## option : path to the input + "header_choice:s" => \$header_choice, ## Presence or not of header in tabular file + "nblineheader:i" => \$nbline_header, ## numbre of header line present in file + "colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file + "delta:f" => \$delta, + "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral) + "output|o:s" => \$out_tab, ## option : path to the ouput (tabular : input+results ) + "view|v:s" => \$out_html, ## option : path to the results view (output2) + "outputxls:s" => \$out_xls, ## option : path to the xls-like format output + ) ; + +#============================================================================= +# EXCEPTIONS +#============================================================================= +$help and &help ; + +#============================================================================= +# MAIN SCRIPT +#============================================================================= + + +## -------------- Conf file ------------------------ : +my ( $CONF ) = ( undef ) ; +foreach my $conf ( <$binPath/*.cfg> ) { + my $oConf = lib::conf::new() ; + $CONF = $oConf->as_conf($conf) ; +} + +## -------------- HTML template file ------------------------ : +foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; } + + +## --------------- Global parameters ---------------- : +my ( $ids, $masses, $results ) = ( undef, undef, undef ) ; +my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ; +my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ; + +## --------------- retrieve input data -------------- : + +## manage only one mass +if ( ( defined $mass ) and ( $mass ne '' ) ) { + my @masses = split(" ", $mass); + $masses = \@masses ; + for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); } +} ## 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 masses and set ids + my $ocsv = lib::csv->new() ; + my $csv = $ocsv->get_csv_object( "\t" ) ; + if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ; } + $masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv + my $nbmz = @$masses ; + for (my $i=1 ; $i<=$nbmz+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); } +} +else { + warn "[warning] Input data are missing : none mass or file of masses\n" ; + &help ; +} + +## ---------------- launch queries -------------------- : + +if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) { + ## prepare masses list and execute query + my $oHmdb = lib::hmdb::new() ; + my $hmdb_pages = undef ; + + $results = [] ; # prepare arrays ref + my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ; + + ## get the hmdb server status by a test query - continuous queries or kill script. + my $status = $oHmdb->test_matches_from_hmdb_ua() ; + $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution + + foreach my $mzs ( @{$submasses} ) { + + my $result = undef ; + my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; + $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; + $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs) ; ## hash format result + + $results = [ @$results, @$result ] ; + } + + ## 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} ) ; + +# print Dumper $results ; +} +else { + croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ; +} ## end ELSE + +## -------------- Produce HTML/CSV output ------------------ : + +if ( ( defined $out_html ) and ( defined $results ) ) { + my $oHtml = lib::hmdb::new() ; + my ($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) ; + 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 { + warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ; +} + +if ( ( defined $out_tab ) and ( defined $results ) ) { + # produce a csv based on METLIN format + my $ocsv = lib::hmdb::new() ; + if (defined $masses_file) { + my $lm_matrix = undef ; + if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) { +# $lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ; + $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ; + $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ; + } + elsif ( ( $header_choice eq 'no' ) ) { +# $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ; + $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ; + $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ; + } + $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ; + } + elsif (defined $mass) { + $ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ; + } +} ## END IF +else { + warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ; +} + +## Write XLS like format +if ( ( defined $out_xls ) and ( defined $results ) ) { + my $ocsv = lib::hmdb::new() ; + $ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ; +} + + +#==================================================================================== +# Help subroutine called with -h option +# number of arguments : 0 +# Argument(s) : +# Return : 1 +#==================================================================================== +sub help { + print STDERR " +help of wsdl_hmdb + +# wsdl_hmdb is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. +# Input : formula or list of formula +# Author : Franck Giacomoni and Marion Landi +# Email : fgiacomoni\@clermont.inra.fr +# Version : 1.4 +# Created : 08/07/2012 +# Updated : 21/01/2016 +USAGE : + wsdl_hmdb.pl -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] + + or + wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] + -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] + + or + wsdl_hmdb.pl -h for help + + "; + exit(1); +} + +## END of script - F Giacomoni + +__END__ + +=head1 NAME + + wsdl_hmdb.pl -- script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. + +=head1 USAGE + + wsdl_hmdb.pl -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] + + or + wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] + -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] + +=head1 SYNOPSIS + +This script manages batch queries on HMDB server. + +=head1 DESCRIPTION + +This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. + +=over 4 + +=item B<function01> + +=item B<function02> + +=back + +=head1 AUTHOR + +Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<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 : 06 / 06 / 2013 + +version 1.2 : 27 / 01 / 2014 + +version 1.3 : 19 / 11 / 2014 + +version 1.4 : 21 / 01 / 2016 - a clean version for community + +=cut \ No newline at end of file