Inheritance diagram for Bio::EnsEMBL::IdMapping::ResultAnalyser:

Public Member Functions
public void	analyse ()

public void	classify_source_genes_by_type ()

public void	classify_genes_by_mapping_simple ()

public void	classify_genes_by_mapping ()

public String	add ()

public String	get ()

public Arrayref	get_all_by_subclass ()

public Arrayref	get_all_by_class ()

public Int	get_count_by_subclass ()

public Int	get_count_by_class ()

public Arrayref	get_all_classes ()

public String	class_key ()

public void	write_results_to_file ()

public void	create_clicklist ()

public void	create_mapping_summary ()

public String	read_from_file ()

Public Member Functions inherited from Bio::EnsEMBL::IdMapping::BaseObject
public $this	new ()

public Filehandle	get_filehandle ()

public Boolean	file_exists ()

public SQLStatement	fetch_value_from_db ()

public Int	dump_table_to_file ()

public Int	upload_file_into_table ()

public Bio::EnsEMBL::Utils::Logger	logger ()

public Bio::EnsEMBL::Utils::ConfParser	conf ()

public Bio::EnsEMBL::IdMapping::Cache	cache ()

Detailed Description

Synopsis

# get a result analyser
my $analyser = Bio::EnsEMBL::IdMapping::ResultAnalyser->new(
  -LOGGER => $logger,
  -CONF   => $conf,
  -CACHE  => $cache
);
 
# analyse results
$analyser->analyse( $gene_mappings,
  $stable_id_mapper->get_all_stable_id_events('similarity') );
 
# write results to file
$analyser->write_results_to_file;
 
# create click lists
$analyser->create_clicklist;
 
# mapping_summary
$analyser->create_mapping_summary;

Description

This is a utility module which analyses the stable Id mapping results
by providing various sorts of mapping statistics. It also creates
clicklists and a mapping summary.

Definition at line 38 of file ResultAnalyser.pm.

Member Function Documentation

◆ add()

public String Bio::EnsEMBL::IdMapping::ResultAnalyser::add ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Arg[2]      : String $class - key identifying a gene type (see class_key())
  Arg[3]      : String $subclass - status identifier (e.g. 'mapped', 'lost')
  Arg[4]      : String $stable_id - gene stable Id
  Arg[5]      : String $val - value (usually 0 or 1)
  Example     :

$analyser->add('source', 'KNOWN-ensembl-protein_coding',

'mapped', 'ENSG00002342', 1);

  Description : Add a stable Id / property pair to a name/dbtype lookup hash.

                The datastructure is a bit of a bloat, but is general enough to
                be used as a lookup hash and to generate statistics (counts by
                type) and debug lists (dump by type).
  Return type : String - the added value
  Exceptions  : none
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ analyse()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::analyse ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::MappingList $gene_mappings - the gene
                mappings to analyse
  Arg[2]      : Arrayref of Strings - similarity events
  Example     :

$analyser->analyse($gene_mappings,

$stable_id_mapper->get_all_stable_id_events('similarity'));

  Description : Analyses the results of a stable Id mapping run.
  Return type : none
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development

Code:

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◆ class_key()

public String Bio::EnsEMBL::IdMapping::ResultAnalyser::class_key ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyGene $gene - a gene object
  Example     :

my $class = $analyser->class_key($gene);

  Description : Generates a key identifying a gene class. This identifier is 
                composed from the gene's logic naame, and biotye.
  Return type : String
  Exceptions  : none
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ classify_genes_by_mapping()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::classify_genes_by_mapping ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::MapppingList $gene_mappings - gene
                mappings to classify
  Arg[2]      : Arrayref of Strings - similarity events
  Example     :

$analyser->classify_genes_by_mapping;

  Description : Classifies genes by mapping. Status is
                  'mapped' => stable Id was mapped
                  'lost_similar' => stable Id not mapped, but there is a
                                    similarity entry for the source Id
                  'lost_definite' => not mapped and no similarity
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : This method is not in use at the momen.
  Status      : At Risk
              : under development

Code:

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◆ classify_genes_by_mapping_simple()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::classify_genes_by_mapping_simple ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::MapppingList $gene_mappings - gene
                mappings to classify
  Example     :

$analyser->classify_genes_by_mapping_simple;

  Description : Classifies target genes by mapping ('mapped' or 'unmapped').
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : This method is not in use at the momen.
  Status      : At Risk
              : under development

Code:

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◆ classify_source_genes_by_type()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::classify_source_genes_by_type ( )

  Example     :

$analyser->classify_source_genes_by_type;

  Description : Classifies source genes by type and adds them to the internal
                datastructure. For the format of the classification string see
                class_key().
  Return type : none
  Exceptions  : none
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ create_clicklist()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::create_clicklist ( )

  Example     :

$analyser->create_clicklist;

  Description : Writes an html file which contains a list of all lost genes,
                with hyperlinks to the appropriate archive website. This is to
                manually check lost genes.
  Return type : none
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

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◆ create_mapping_summary()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::create_mapping_summary ( )

  Example     :

$analyser->create_mapping_summary();

  Description : Writes a text file containing a summary of the mapping stats.
                This will be emailed to the genebuilder for evaluation (you will
                have to manually send the email, using the text in
                "mapping_summary.txt" as the template).
  Return type : none
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

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sub create_mapping_summary {
  my $self = shift;
  
  my $fh = $self->get_filehandle('mapping_summary.txt');
 
  #
  # title
  # 
  print $fh qq(Stable ID mapping results\n);
  print $fh qq(=========================\n\n);
 
  #
  # timing
  #
  print $fh "Run at:  ".localtime()."\n";
  print $fh "Runtime: ";
  print $fh $self->logger->runtime, "\n\n";
 
  #
  # parameters used for this run
  #
  print $fh $self->conf->list_param_values;
  print $fh "\n";
 
  #
  # mapping stats
  #
  foreach my $type (qw(exon transcript translation gene gene_detailed)) {
    my $filename = "${type}_mapping_stats.txt";
    
    if ($self->file_exists($filename, 'stats')) {
      print $fh $self->read_from_file($filename, 'stats');
      print $fh "\n\n";
    } else {
      print $fh "No mapping stats found for $type.\n\n";
    }
  }
 
  #
  # db uploads
  #
  my @uploads = (
    ['stable_ids'  => 'Stable IDs'],
    ['events'      => 'Stable ID events and mapping session'],
    ['archive'     => 'Gene and peptide archive'],
  );
  
  my $fmt1 = "%-40s%-20s\n";
 
  print $fh qq(Data uploaded to db:\n);
  print $fh qq(====================\n\n);
 
  if ($self->conf->param('dry_run')) {
   
    print $fh "None (dry run).\n";
  
  } else {
  
    foreach my $u (@uploads) {
      my $uploaded = 'no';
      $uploaded = 'yes' if ($self->conf->is_true("upload_".$u->[0]));
      print $fh sprintf($fmt1, $u->[1], $uploaded);
    }
    
  }
 
  print $fh "\n";
 
  #
  # stats and clicklist
  #
  my @output = (
    ['stats'    => 'statistics (including clicklists of deleted IDs)'],
    ['debug'    => 'detailed mapping output for debugging'],
    ['tables'   => 'data files for db upload'],
  );
  
  my $fmt2 = "%-20s%-50s\n";
 
  print $fh qq(\nOutput directories:\n);
  print $fh qq(===================\n\n);
 
  print $fh sprintf($fmt2, qw(DIRECTORY DESCRIPTION));
  print $fh ('-'x72), "\n";
 
  print $fh sprintf($fmt2, 'basedir', $self->conf->param('basedir'));
 
  foreach my $o (@output) {
    print $fh sprintf($fmt2, '$basedir/'.$o->[0], $o->[1]);
  }
 
  print $fh "\n";
 
  #
  # clicklist of first 10 deleted genes
  #
  print $fh qq(\nFirst 10 deleted known genes:\n);
  print $fh qq(=============================\n\n);
 
  my $in_fh = $self->get_filehandle('genes_lost.txt', 'debug', '<');
  my $prefix = $self->conf->param('urlprefix');
  my $i;
  
  while (<$in_fh>) {
    last if (++$i > 10);
    
    chomp;
    my ($stable_id, $type) = split(/\s+/);
    
    next unless ($type eq 'known');
 
    print $fh sprintf($fmt2, $stable_id, "${prefix}$stable_id");
  }
 
  close($in_fh);
  close($fh);
}

◆ get()

public String Bio::EnsEMBL::IdMapping::ResultAnalyser::get ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Arg[2]      : String $class - key identifying a gene type (see class_key())
  Arg[3]      : String $subclass - status identifier (e.g. 'mapped', 'lost')
  Arg[4]      : String $stable_id - gene stable Id
  Example     :

my $mapping_status = $analyser->get('source',

'KNOWN-ensembl-protein_coding', 'mapped', 'ENSG00002342');

  Description : Gets a stable Id mapping status from the internal datastructure.
  Return type : String
  Exceptions  : none
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ get_all_by_class()

public Arrayref Bio::EnsEMBL::IdMapping::ResultAnalyser::get_all_by_class ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Arg[2]      : String $class - key identifying a gene type (see class_key())
  Example     :

my @stable_ids = @{
                 $analyser->get_all_by_class( 'source',
                   'KNOWN-ensembl-protein_coding' ) };

  Description : Gets a list of stable Id for a given class.
  Return type : Arrayref of String (stable Ids)
  Exceptions  : thrown on missing arguments
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ get_all_by_subclass()

public Arrayref Bio::EnsEMBL::IdMapping::ResultAnalyser::get_all_by_subclass ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Arg[2]      : String $class - key identifying a gene type (see class_key())
  Arg[3]      : String $subclass - status identifier (e.g. 'mapped', 'lost')
  Example     :

my @mapped_stable_ids = @{
                 $analyser->get_all_by_subclass(
                   'source', 'KNOWN-ensembl-protein_coding',
                   'mapped'
                 ) };

  Description : Gets a list of stable Id for a given subclass.
  Return type : Arrayref of String (stable Ids)
  Exceptions  : thrown on missing arguments
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ get_all_classes()

public Arrayref Bio::EnsEMBL::IdMapping::ResultAnalyser::get_all_classes ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Example     :

foreach my $class (@{ $analyser->get_all_classes('source') }) {
                 print "$class\n";
               }

  Description : Gets a list of classes in the ResultAnalyser.
  Return type : Arrayref of String
  Exceptions  : thrown on missing argument
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ get_count_by_class()

public Int Bio::EnsEMBL::IdMapping::ResultAnalyser::get_count_by_class ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Arg[2]      : String $class - key identifying a gene type (see class_key())
  Example     :

my $num_mapped = $analyser->get_count_by_class('source',

'KNOWN-ensembl-protein_coding');

  Description : Gets the number of stable Ids for a given class.
  Return type : Int
  Exceptions  : thrown on missing arguments
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ get_count_by_subclass()

public Int Bio::EnsEMBL::IdMapping::ResultAnalyser::get_count_by_subclass ( )

  Arg[1]      : String $dbtype - db type ('source' or 'target')
  Arg[2]      : String $class - key identifying a gene type (see class_key())
  Arg[3]      : String $subclass - status identifier (e.g. 'mapped', 'lost')
  Example     :

my $num_mapped = $analyser->get_count_by_subclass('source',

'KNOWN-ensembl-protein_coding', 'mapped');

  Description : Gets the number of stable Ids for a given subclass.
  Return type : Int
  Exceptions  : thrown on missing arguments
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ read_from_file()

public String Bio::EnsEMBL::IdMapping::ResultAnalyser::read_from_file ( )

  Arg[1]      : String $filename - name of file to read
  Arg[2]      : (optional) String $append - directory name to append to basedir
  Example     :

my $stats_text = $analyser->read_from_file('gene_mapping_stats',

'stats');

  Description : Reads mapping stats from a file.
  Return type : String
  Exceptions  : none
  Caller      : internal
  Status      : At Risk
              : under development

Code:

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◆ write_results_to_file()

public void Bio::EnsEMBL::IdMapping::ResultAnalyser::write_results_to_file ( )

  Example     :

$analyser->write_results_to_file;

  Description : Writes the results of the result analysis to a file. This is a 
                human-readable text detailing the mapping statistics.
  Return type : none
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

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The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ add()

◆ analyse()

◆ class_key()

◆ classify_genes_by_mapping()

◆ classify_genes_by_mapping_simple()

◆ classify_source_genes_by_type()

◆ create_clicklist()

◆ create_mapping_summary()

◆ get()

◆ get_all_by_class()

◆ get_all_by_subclass()

◆ get_all_classes()

◆ get_count_by_class()

◆ get_count_by_subclass()

◆ read_from_file()

◆ write_results_to_file()