#!/usr/local/bin/perl ############################################################################### # Basic SBEAMS setup ############################################################################### use strict; use FindBin; use Data::Dumper; use File::Basename; use lib "$FindBin::Bin/../../lib/perl"; use vars qw ($q $sbeams $sbeamsMOD $PROG_NAME $current_username $modification_helper ); use SBEAMS::Connection qw($q $log); use SBEAMS::Connection::Settings; use SBEAMS::Connection::Tables; use SBEAMS::PeptideAtlas; use SBEAMS::PeptideAtlas::Settings; use SBEAMS::PeptideAtlas::Tables; use SBEAMS::PeptideAtlas::ModificationHelper; use SBEAMS::PeptideAtlas::ConsensusSpectrum; use SBEAMS::Proteomics::SpecViewer; my $denormalize = 0; my $curveType = 'function'; my $error_state = 0; $sbeams = new SBEAMS::Connection; $sbeamsMOD = new SBEAMS::PeptideAtlas; $sbeamsMOD->setSBEAMS($sbeams); my $consensus = new SBEAMS::PeptideAtlas::ConsensusSpectrum; $consensus->setSBEAMS($sbeams); $PROG_NAME="ShowOneSpectrum"; ############################################################################### # Define global variables if any and execute main() ############################################################################### my $ymax = 10; main(); ############################################################################### # Main Program: # # If $sbeams->Authenticate() succeeds, print header, process the CGI request, # print the footer, and end. ############################################################################### sub main { #### Do the SBEAMS authentication and exit if a username is not returned exit unless ($current_username = $sbeams->Authenticate( permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin', 'PeptideAtlas_readonly', 'PeptideAtlas_exec'], #connect_read_only=>1, allow_anonymous_access=>1, )); #### Print the header, figure and do what the user want, and print footer my %parameters; $sbeams->parse_input_parameters(q=>$q,parameters_ref=>\%parameters); $sbeams->processStandardParameters(parameters_ref=>\%parameters); my $spectrum = get_consensus( %parameters ); # die Dumper $spectrum; my @peak_array; my $content = $sbeams->makeInfoText( "Spectrum unavailable" ); if ( $spectrum->{intensities} ) { for ( my $i = 0; $i < scalar( @{$spectrum->{intensities}} ); $i++ ) { push @peak_array, [$spectrum->{masses}->[$i], $spectrum->{intensities}->[$i]]; } my $start_scan = 1; my $spectrum_name = $spectrum->{modified_sequence} . '+' . $spectrum->{charge}; $content = ""; $parameters{peakDetect} ||= 'true'; #### Lorikeet me! ################################################## my $lorikeet = new SBEAMS::Proteomics::SpecViewer; my $lorispectrum = $lorikeet->generateSpectrum( charge => $spectrum->{charge}, modified_sequence => $spectrum->{modified_sequence}, precursor_mass => $spectrum->{mz}, scan => $start_scan, name => $spectrum->{library_name}, a_ions => $parameters{'ShowA'}, b_ions => $parameters{'ShowB'}, c_ions => $parameters{'ShowC'}, x_ions => $parameters{'ShowX'}, y_ions => $parameters{'ShowY'}, peakDetect => $parameters{'peakDetect'}, z_ions => $parameters{'ShowZ'}, spectrum => \@peak_array ); $content .= ""; $content .= "

$lorispectrum

\n"; } if ( $parameters{plot_only} && $parameters{plot_only} =~ /true/i ) { print $sbeams->get_http_header(); print ""; print $content; print ""; } else { $sbeamsMOD->display_page_header(); print $content; $sbeamsMOD->display_page_footer(); } # $sbeams->display_page_footer(close_tables=>'YES', # separator_bar=>'YES',display_footer=>'NO'); } # end main sub get_consensus { my %parameters = @_; my $sql = qq~ SELECT sequence,charge,mz_exact,protein_name, protein_name_alt,modified_sequence, consensus_library_name, file_path, entry_idx FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM CLS JOIN $TBAT_CONSENSUS_LIBRARY CL ON CL.consensus_library_id = CLS.consensus_library_id WHERE consensus_library_spectrum_id = '$parameters{consensus_library_spectrum_id}' ~; my @rows = $sbeams->selectSeveralColumns($sql); foreach my $row (@rows) { my ($seq, $chg, $mz, $pn, $pn_alt, $mod_seq, $lib_name, $file_path, $entry_idx ) = @{$row}; $parameters{'peptide'} = $seq; $parameters{'charge'} = $chg; $parameters{'precursor_mass'} = $mz; $parameters{'protein_name'} = $pn; $parameters{'protein_name_alt'} = $pn_alt; $parameters{'modified_sequence'} = $mod_seq; $parameters{'library_name'} = $lib_name; $parameters{'file_path'} = $file_path; $parameters{'entry_idx'} = $entry_idx; } my %results; $results{modified_sequence} = $parameters{modified_sequence}; $results{charge} = $parameters{charge}; $results{mz} = $parameters{'precursor_mass'}; $results{lib_desc} = "$parameters{library_name}"; $results{lib_desc} =~ s/\.sptxt//; my $peptide = $parameters{peptide}; $peptide =~ s/^.\.//; $peptide =~ s/\..$//; my $precursor_mass = $parameters{'precursor_mass'}; my $charge = $parameters{'charge'}; my $protein_name = $parameters{'protein_name'}; my $protein_name_alt = $parameters{'protein_name_alt'}; my $modified_sequence = $parameters{'modified_sequence'}; $parameters{assumed_charge} = $charge; ## if no modified_sequence, use unmodified sequence unless ($modified_sequence) { $modified_sequence = $parameters{peptide}; } #### Calculate peptide mass information my $masstype = $parameters{masstype} || 0; $modification_helper = new SBEAMS::PeptideAtlas::ModificationHelper(); my $peaks; if ( $parameters{file_path} ) { if ( -e $parameters{file_path} ) { $peaks = $consensus->get_spectrum_peaks( %parameters, denormalize => 0, strip_unknowns => 1 ); } else { $peaks = $consensus->get_spectrum_peaks( %parameters, denormalize => 0, strip_unknowns => 1, use_gzipped => 1 ); } } else { $peaks = get_db_peaks($parameters{consensus_library_spectrum_id}); } $peaks->{mz} = $results{mz}; $peaks->{modified_sequence} = $results{modified_sequence}; $peaks->{charge} = $results{charge}; for my $param ( keys( %parameters ) ) { $peaks->{$param} ||= $parameters{$param}; } return $peaks; } # end get_consensus sub get_db_peaks { my $library_spectrum_id = shift || return undef; #### Extract the actual mass,intensity pairs from database my $sql = "SELECT mz, relative_intensity ". " FROM $TBAT_CONSENSUS_LIBRARY_SPECTRUM_PEAK ". " WHERE consensus_library_spectrum_id = '$library_spectrum_id'"; my $sth = $sbeams->get_statement_handle($sql); my %peaks = ( intensities => [], masses => [] ); while ( my @row = $sth->fetchrow_array() ) { push @{$peaks{intensities}}, $row[1]; push @{$peaks{masses}}, $row[0]; } return \%peaks; } __DATA__