#!/usr/local/bin/perl
###############################################################################
# $Id: $
#
# SBEAMS is Copyright (C) 2000-2017 Institute for Systems Biology
# This program is governed by the terms of the GNU General Public License (GPL)
# version 2 as published by the Free Software Foundation. It is provided
# WITHOUT ANY WARRANTY. See the full description of GPL terms in the
# LICENSE file distributed with this software.
###############################################################################
###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
#use vars qw ($sbeams);
use lib qw (../../lib/perl);
#use CGI::Carp qw(fatalsToBrowser croak);
use Data::Dumper;
use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::DataTable;
use SBEAMS::Connection::GoogleVisualization;
use SBEAMS::Connection::TabMenu;
use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;
###############################################################################
# Global Variables
###############################################################################
my $sbeams = new SBEAMS::Connection;
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);
# Read input parameters
my $params = process_params();
my $show_image = 0;
{ # Main
# Authenticate or exit
my $username = $sbeams->Authenticate( allow_anonymous_access => 1) || exit;
## get current settings
my $project_id = $sbeams->getCurrent_project_id();
my $list_help = get_table_help( table => 'list' );
my $protein_help = get_table_help( table => 'protein' );
my $page = $sbeams->getGifSpacer( 700 ) . " \n";
# Get the HTML to display the tabs
my $tabMenu = $atlas->getTabMenu(
parameters_ref => $params,
program_name => 'PTMList',
);
$page .=<<" END";
$tabMenu
$list_help
END
# Add general section
$page .= get_list_selector();
$page .= get_list_overview();
$page .= "
";
# $page .= get_list_table();
# Print what we already have, speed up apparent page loading time.
$atlas->display_page_header( onload => "set_toggle_box( 'protein_list_table' );sortables_init()", sortable => 1 );
print $page;
$atlas->display_page_footer();
} # end main
sub get_table_help {
my %args = @_;
my $name = $args{table};
return '' unless $name;
$args{mode} ||= 'section';
my @entries;
my $hidetext;
my $showtext;
my $heading;
my $description;
if ( $name eq 'build' ) {
@entries = ( { key => 'Build Name', value => 'The simple name for this build, usually contains organism, prophet cutoff, and other information. ' },
{ key => 'Build Description', value => 'More detailed information about build. ' },
{ key => 'Reference Database', value => 'Database to which peptides were mapped, generally different than search database. This mapping is done by running BLAST, and allows the peptides to be mapped the the organism\'s genomic sequence. ' },
{ key => 'Build Date', value => 'Date upon which build was finished. ' },
{ key => '# Samples', value => 'The number of individual samples which comprise this build. Each sample contains one or more LCMS/MS runs, and generally corresponds to a single scientific experiment.' } ,
{ key => 'Distinct Peptides', value => 'This shows the number of distinct peptide sequences that were seen in this build. Observations of the peptide in different charge states or with different modifications are coalesced.' } ,
{ key => 'Total Observations ', value => 'The total number of spectra that yeilded identifications above the build threshold. Observations of the same base peptide sequences multiple times or in various charge states/modifications, whould each contribute to the total' }
);
$showtext = 'show row descriptions';
$hidetext = 'hide row descriptions';
$heading = 'Build Overview';
$description= 'These values pertain to the atlas build as a whole';
} elsif ( $name eq 'batch' ) {
@entries = ( { key => 'ID', value => 'Database ID for this sample (search batch) ' },
{ key => 'Sample_Name', value => 'Simple name for this sample/experiment. ' },
{ key => '#_Spectra_Searched', value => 'The total number of spectra searched in the sample. ' },
{ key => "#_Spectra_ID'd", value => 'The number of spectra identifed with a probability greater than the atlas threshold ' },
{ key => '#_Distinct', value => 'The number of distinct peptide sequences, seen more than once (multiobs), in this build that are seen in this sample. ' },
{ key => '#_Unique', value => "The number of distinct, multiobs peptides that are seen only in this sample (unique contribution). This discriminates against smaller samples, and is less useful in atlas' with a large number of samples. " },
{ key => '#_Progressive', value => 'Order-dependent unique multiobs peptides contributed by a given sample. The contribution for each sample is based on the samples that have gone before it, so later samples tend to have a lower progressive contribution. ' },
{ key => '#_Cumulative', value => 'Order-dependent cumulative number of unique multiobs peptides contributed to build by this and previous samples. ' },
{ key => '#_Proteins', value => 'The number of canonical (highly distinguishable, non-redundant) protein sequences identified from the peptides in this sample.' },
{ key => '#_Cum_Prots', value => 'Order-dependent cumulative number of canonical proteins contributed to build by this and previous samples. Counts non-human contaminants, so final tally may be greater than Canonical Proteins count in Build Overview. ' },
# { key => 'Sens', value => 'The sensitivity of the Peptide Prophet model at a probablility of 0.9, the percent of true positives that would be included at that threshold was used as a cutoff. ' },
{ key => 'FDR_(%)', value => 'The error rate of peptides above the threshold Peptide Prophet model at a probablility of 0.9, the percent of false positives that would be included at the build threshold. ' },
{ key => 'Sample_Date', value => ''},
);
$heading = 'Sample Overview';
$description = 'These values pertain to individual samples within the atlas';
} elsif ( $name eq 'mayu' ) {
@entries = ( { key => 'nr_runs', value => 'Number of MS runs contributing to this build '},
{ key => 'nr_files', value => 'Always 1 '},
{ key => 'mFDR', value => 'Data in current row applies to all data meting this PSM (spectrum) FDR threshold. '},
{ key => 'target_PSM', value => 'Number of non-decoy PSMs at this mFDR (counts peptides mappable to protein reference set only)'},
{ key => 'decoy_PSM', value => 'Number of decoy PSMs at this mFDR '},
{ key => 'FP_PSM', value => 'Number of false positive PSMs predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
{ key => 'TP_PSM', value => 'target_PSM - FP_PSM '},
{ key => 'target_pepID', value => 'Number of non-decoy unique peptides at this mFDR (counts peptides mappable to protein reference set only) '},
{ key => 'decoy_pepID', value => 'Number of decoy unique peptides at this mFDR '},
{ key => 'FP_pepID', value => 'Number of false positive unique peptides predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
{ key => 'FP_pepID_stdev', value => ' '},
{ key => 'TP_pepID', value => 'target_pepID - FP_pepID '},
{ key => 'pepFDR', value => 'Peptide FDR (unique peptides)'},
{ key => 'target_protID', value => 'Number of non-decoy protein identifications at this mFDR. Applied to the covering set of proteins -- a set that is close to the smallest necessary to explain all the pepIDs. Includes all canonicals and some possibly_distinguished. '},
{ key => 'decoy_protID', value => 'Number of decoy protein identifications at this mFDR. '},
{ key => 'FP_protID', value => 'Number of false postiive protein identifications predicted by Mayu for this mFDR. Usually near, but not exactly the same as, the number of decoys. '},
{ key => 'FP_protID_stdev', value => ' '},
{ key => 'TP_protID', value => 'target_protID - FP_protID '},
{ key => 'protFDR', value => 'Protein FDR. The largest value in this column is the protein FDR for the entire build. '},
{ key => 'lFDR1, lFDR5, lFDR10,2 lFDR5', value => 'Local protein FDR, computed over the previous step (i.e. between the previous row in the table and the current row), the previous 5 steps, the previous 10 steps, and the previous 25 steps. Often there are fewer than 25 rows in the table, in which case column lFDR25 is uninformative. '},
{ key => 'target_protIDs, decoy_protIDs, etc.', value => 'Same as above, except for singleton proteins (those identified by only one PSM) only. '},
{ key => 'target_protIDns, decoy_protIDns, etc.', value => 'Same as above, except for multiply-observed proteins only. '},
);
$heading = 'Mayu';
$description = 'Reiter L, Claassen M, et al., Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry, Mol Cell Proteomics. 2009 Nov;8(11):2405-17 ';
}
return unless @entries;
return \@entries if $args{mode} eq 'entries_only';
my $help = $atlas->get_table_help_section( name => $name,
description => $description,
heading => $heading,
entries => \@entries,
showtext => $showtext,
hidetext => $hidetext );
return $help;
} # end get_table_help
# General list information
sub get_list_overview {
my $build_id = shift;
# Get a list of accessible project_ids
my @project_ids = $sbeams->getAccessibleProjects();
my $project_ids = join( ",", @project_ids ) || '0';
my $sql = qq~
SELECT DPL.title AS list_title, description, n_ptm, original_file, url,
image_path, abstract, contributors, ptm_list_id, image_caption,
pubmed_id
FROM $TBAT_PTM_LIST DPL
WHERE ptm_list_id > 0
AND DPL.record_status <> 'D'
AND project_id IN ( $project_ids );
~;
my $table = "
\n";
my $sth = $sbeams->get_statement_handle( $sql );
while( my $info = $sth->fetchrow_hashref() ) {
for my $key ( keys( %{$info} ) ) {
$info->{lc($key)} = $info->{$key};
}
my $spc = $sbeams->getGifSpacer(5);
my $tab = $sbeams->getGifSpacer(20);
my $contributor = $atlas->encodeSectionItem( key => 'Contributors',
value => "$info->{contributors}" . $spc, vspan => 3 ) . "\n";
$contributor =~ s/NOWRAP/>$tab<\/TD>
info( "contributor is $contributor" );
my $desc = $atlas->encodeSectionItem( key => 'Description',
value => $info->{description}, vspan => 3 ) . "\n";
$desc =~ s/NOWRAP/>$tab<\/TD>
encodeSectionItem( key => 'Number of Proteins',
value => $info->{n_proteins}, vspan => 3 ) . "\n";
$nprot =~ s/NOWRAP/>$tab<\/TD>
\n";
}
$table .= "\n";
return $table;
}
# Peptide build stats
sub get_list_table {
my $build_id = shift;
# Get a list of accessible project_ids
my @project_ids = $sbeams->getAccessibleProjects();
my $project_ids = join( ",", @project_ids ) || '0';
my $table = "
\n";
my $sql =<<" END";
SELECT list_protein_id, uniprot_accession, protein_symbol, original_name, protein_full_name, gene_symbol, comment, priority
FROM $TBAT_PTM_LIST_ENTRY
WHERE ptm_list_id = $params->{ptm_list_id}
ORDER BY uniprot_accession ASC
END
my @samples;
my $sth = $sbeams->get_statement_handle( $sql );
while( my @row = $sth->fetchrow_array() ) {
$row[0] = "";
$row[3] ||= $row[1];
$row[7] = $sbeams->makeInfoText( "n/a" );
$row[4] = $sbeams->truncateStringWithMouseover( string => $row[4], len => 60, nowrap => 1 );
$row[6] = $sbeams->truncateStringWithMouseover( string => $row[6], len => 60 );
push @samples, \@row;
}
my $dag = '†';
my @headings = ( "" => 'list_protein_id',
UniProt => 'uniprot_accession',
ProteinSymbol => 'protein_symbol',
OriginalName => 'original_name',
ProteinFullName => 'protein_full_name',
GeneSymbol => 'gene_symbol',
Comment => 'comment',
Priority => 'priority'
);
# for my $h ( @headings ) {
# $log->info( $h );
# }
my $headings_ref = $atlas->make_sort_headings( headings => \@headings, default => 'UniProt', asc => 1 );
# $table .= $atlas->encodeSectionHeader(
# text => 'List Proteins',
# width => 920
# );
my $table = SBEAMS::Connection::DataTable->new( class => 'scrolltable',
id => 'protein_list_table',
'__use_thead' => 1 );
$table->addRow( $headings_ref );
$table->setRowAttr( ROWS => [1], BGCOLOR => '#0000A0', CLASS => 'sortheader' );
my $rnum = 2;
for my $row ( @samples ) {
$table->addRow( $row );
$table->setRowAttr( ROWS => [$rnum], BGCOLOR => '#EAEAEA' );
$rnum++;
}
# $atlas->encodeSectionTable( rows => [ $headings_ref, @samples ],
# header => 1,
# nowrap => [1..scalar(@headings)],
# table_id => 'protein_list_table',
# class => 'scrolltable',
# align => [ qw(center left right right right right right right right right right center) ],
# bg_color => '#EAEAEA',
# sortable => 1 );
# $table =~ s/(
)/$1<\/THEAD>/m;
# die Dumper( $table );
my $btxt = get_btxt( qw( Selected All Uncheck Check Search ) );
# die Dumper( $btxt );
my $fbox_help = '
' . $sbeams->makeInfoText( "Text entered into the box will filter the protein list (all fields)" ) . '
';
my $cbox_help = '
' . $sbeams->makeInfoText( "Use these buttons to check or uncheck the visible proteins" ) . '
';
my $show_help = '
' . $sbeams->makeInfoText( "Use these buttons to show all your selected proteins or the entire list (resets filter box)" ) . '
';
my $submit_help = '
' . $sbeams->makeInfoText( "This will submit your list of selected proteins to the SRM Atlas for a transitions query" ) . '
';
my $spc = ' ' x 3;
my $fbox = "Filter List: $spc";
my $submit = "SRM Atlas: $spc";
my $show = "Show: $spc";
my $build_id = ( $sbeams->isGuestUser() ) ? 120 : 146;
my $form = qq~