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Bio::EnsEMBL::Utils::ConversionSupport Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::ConversionSupport:

List of all members.


Class Summary

Synopsis

  my $serverroot = '/path/to/ensembl';
  my $support = new Bio::EnsEMBL::Utils::ConversionSupport($serverroot);

  # parse common options
  $support-\>parse_common_options;

  # parse extra options for your script
  $support-\>parse_extra_options( 'string_opt=s', 'numeric_opt=n' );

  # ask user if he wants to run script with these parameters
  $support-\>confirm_params;

  # see individual method documentation for more stuff

Definition at line 30 of file ConversionSupport.pm.

Available Methods

protected Values _by_chr_num ()
protected Attrib_type _get_attrib_id ()
public Array allowed_params ()
public Boolean check_required_params ()
public Boolean comma_to_list ()
public A commify ()
public Boolean confirm_params ()
public String create_commandline_options ()
public String date ()
public String date_and_mem ()
public date_format ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
dba ()
public Boolean dynamic_use ()
public String error ()
public Arrayref fetch_non_hidden_slices ()
public Filehandle filehandle ()
public Boolean finish_log ()
public Arrayref fix_attrib_value ()
public get_attrib_values ()
public Hashref get_chrlength ()
public Array get_common_params ()
public DBAdaptor get_database ()
public DBI get_dbconnection ()
public Hashref get_ensembl_chr_mapping ()
public Array get_loutre_params ()
public Arrayref get_non_hidden_slice_names ()
public String get_species_scientific_name ()
public Int get_taxonomy_id ()
public Arrayref get_unique_genes ()
public Arrayref get_wanted_chromosomes ()
public Filehandle init_log ()
public String list_all_params ()
public Boolean list_or_file ()
public Boolean log ()
public void log_error ()
public Filehandle log_filehandle ()
public Boolean log_stamped ()
public Boolean log_verbose ()
public Boolean log_warning ()
public String mem ()
public
Bio::EnsEMBL::Utils::ConversionSupport 
new ()
public Scalar param ()
public Boolean parse_common_options ()
public Boolean parse_extra_options ()
public String read_user_input ()
public void remove_vega_params ()
public String serverroot ()
public List sort_chromosomes ()
public String species ()
public Hashref split_chromosomes_by_size ()
public Array_ref store_new_attribute ()
public Array_ref update_attribute ()
public user_confirm ()
public Boolean user_proceed ()
public Int warnings ()

Method Documentation

protected Values Bio::EnsEMBL::Utils::ConversionSupport::_by_chr_num ( )
  Example     : my @sorted = sort _by_chr_num qw(X, 6-COX, 14, 7);
  Description : Subroutine to use in sort for sorting chromosomes. Sorts
                numerically, then alphabetically
  Return type : values to be used by sort
  Exceptions  : none
  Caller      : internal ($self->sort_chromosomes)
 
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protected Attrib_type Bio::EnsEMBL::Utils::ConversionSupport::_get_attrib_id ( )
  Arg[1]      : attrib_type.code 
  Arg[2]      : database handle 
  Example     : $self->_get_attrib_id('name',$dbh)
  Description : get attrib_type.attrib_type_id from a attrib_type.code
  Return type : attrib_type.attrib_type_id 
  Caller      : internal
  Status      : stable
 
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public Array Bio::EnsEMBL::Utils::ConversionSupport::allowed_params ( )
  Arg[1-N]    : (optional) List of allowed parameters to set
  Example     : my @allowed = $self->allowed_params(qw(param1 param2));
  Description : Getter/setter for allowed parameters. This is used by
                $self->confirm_params() to avoid cluttering of output with
                conffile entries not relevant for a given script. You can use
                $self->get_common_params() as a shortcut to set them.
  Return type : Array - list of allowed parameters
  Exceptions  : none
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::check_required_params ( )
  Arg[1-N]    : List @params - parameters to check
  Example     : $self->check_required_params(qw(dbname host port));
  Description : Checks $self->param to make sure the requested parameters
                have been set. Dies if parameters are missing.
  Return type : true on success
  Exceptions  : none
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::comma_to_list ( )
  Arg[1-N]    : list of parameter names to parse
  Example     : $support->comma_to_list('chromosomes');
  Description : Transparently converts comma-separated lists into arrays (to
                allow different styles of commandline options, see perldoc
                Getopt::Long for details). Parameters are converted in place
                (accessible through $self->param('name')).
  Return type : true on success
  Exceptions  : none
  Caller      : general
 
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public A Bio::EnsEMBL::Utils::ConversionSupport::commify ( )
  Arg[1]      : Int $num - a number to commify
  Example     : print "An easy to read number: ".$self->commify(100000000);
                # will print 100,000,000
  Description : put commas into a number to make it easier to read
  Return type : a string representing the commified number
  Exceptions  : none
  Caller      : general
  Status      : stable
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::confirm_params ( )
  Example     : $support->confirm_params;
  Description : Prints a table of parameters that were collected from config
                file and commandline and asks user to confirm if he wants
                to proceed.
  Return type : true on success
  Exceptions  : none
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::create_commandline_options ( )
  Arg[1]      : Hashref $settings - hashref describing what to do
                Allowed keys:
                    allowed_params => 0|1   # use all allowed parameters
                    exclude => []           # listref of parameters to exclude
                    replace => {param => newval} # replace value of param with
                                                 # newval
  Example     : $support->create_commandline_options({
                    allowed_params => 1,
                    exclude => ['verbose'],
                    replace => { 'dbname' => 'homo_sapiens_vega_33_35e' }
                });
  Description : Creates a commandline options string that can be passed to any
                other script using ConversionSupport.
  Return type : String - commandline options string
  Exceptions  : none
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::date ( )
  Example     : print "Date: " . $support->date . "\\n";
  Description : Prints a nicely formatted timestamp (YYYY-DD-MM hh:mm:ss)
  Return type : String - the timestamp
  Exceptions  : none
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::date_and_mem ( )
  Example     : print LOG "Time, memory usage: ".$support->date_and_mem."\\n";
  Description : Prints a timestamp and the memory usage of your script.
  Return type : String - timestamp and memory usage
  Exceptions  : none
  Caller      : general
 
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public Bio::EnsEMBL::Utils::ConversionSupport::date_format ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::Utils::ConversionSupport::dba ( )
  Arg[1]      : (optional) String $database - type of db apaptor to retrieve
  Example     : my $dba = $support->dba;
  Description : Getter for database adaptor. Returns default (i.e. created
                first) db adaptor if no argument is provided.
  Return type : Bio::EnsEMBL::DBSQL::DBAdaptor or Bio::Otter::DBSQL::DBAdaptor
  Exceptions  : none
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::dynamic_use ( )
  Arg [1]    : String $classname - The name of the class to require/import
  Example    : $self->dynamic_use('Bio::EnsEMBL::DBSQL::DBAdaptor');
  Description: Requires and imports the methods for the classname provided,
               checks the symbol table so that it doesnot re-require modules
               that have already been required.
  Returntype : true on success
  Exceptions : Warns to standard error if module fails to compile
  Caller     : internal
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::error ( )
  Arg[1]      : (optional) String - error message
  Example     : $support->error("An error occurred: $\@");
                exit(0) if $support->error;
  Description : Getter/setter for error messages
  Return type : String - error message
  Exceptions  : none
  Caller      : general
 
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public Arrayref Bio::EnsEMBL::Utils::ConversionSupport::fetch_non_hidden_slices ( )
  Arg[1]      : B::E::SliceAdaptor
  Arg[2]      : B::E::AttributeAdaptor
  Arg[3]      : string $coord_system_name (optional) - 'chromosome' by default
  Arg[4]      : string $coord_system_version (optional) - 'otter' by default
  Example     : $chroms = $support->fetch_non_hidden_slice($sa,$aa);
  Description : retrieve all slices from a loutre database that don't have a hidden attribute.
                Doesn't retrieve non-reference slices
  Return type : arrayref
  Caller      : general
  Status      : stable
 
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public Filehandle Bio::EnsEMBL::Utils::ConversionSupport::filehandle ( )
  Arg[1]      : String $mode - file access mode
  Arg[2]      : String $file - input or output file
  Example     : my $fh = $support->filehandle('>>', '/path/to/file');
                # print to the filehandle
                print $fh 'Your text goes here...\n';
  Description : Returns a filehandle (*STDOUT for writing, *STDIN for reading
                by default) to print to or read from.
  Return type : Filehandle - the filehandle
  Exceptions  : thrown if file can't be opened
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::finish_log ( )
  Example     : $support->finish_log;
  Description : Writes footer information to a logfile. This includes the
                number of logged warnings, timestamp and memory footprint.
  Return type : TRUE on success
  Exceptions  : none
  Caller      : general
 
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public Arrayref Bio::EnsEMBL::Utils::ConversionSupport::fix_attrib_value ( )
  Arg[1]      : Arrayref of existing B::E::Attributes
  Arg[2]      : dbID of object
  Arg[3]      : name of object (just for reporting)
  Arg[4]      : attrib_type.code
  Arg[5]      : attrib_type.value
  Arg[6]      : interactive ? (0 by default)
  Arg[7]      : table
  Example     : $support->fix_attrib_value($attribs,$chr_id,$chr_name,'vega_export_mod','N',1);
  Description : adds a new attribute to an object, or updates an existing attribute with a new value
                Can be run in interactive or non-interactive mode (default)
  Return type : arrayref of results
  Caller      : general
  Status      : only ever tested with seq_region_attributes to date
 
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public Bio::EnsEMBL::Utils::ConversionSupport::get_attrib_values ( )

Undocumented method

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public Hashref Bio::EnsEMBL::Utils::ConversionSupport::get_chrlength ( )
  Arg[1]      : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Arg[2]      : (optional) String $version - coord_system version
  Arg[3]      : (optional) String $type - type of region eg chromsome (defaults to 'toplevel')
  Arg[4]      : (optional) Boolean - return non reference slies as well (required for haplotypes eq 6-COX)
  Example     : my $chr_length = $support->get_chrlength($dba);
  Description : Get all chromosomes and their length from the database. Return
                chr_name/length for the chromosomes the user requested (or all
                chromosomes by default)
  Return type : Hashref - chromosome_name => length
  Exceptions  : thrown if not passing a Bio::EnsEMBL::DBSQL::DBAdaptor
  Caller      : general
 
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public Array Bio::EnsEMBL::Utils::ConversionSupport::get_common_params ( )
  Example     : my @allowed_params = $self->get_common_params, 'extra_param';
  Description : Returns a list of commonly used parameters in the conversion
                scripts. Shortcut for setting allowed parameters with
                $self->allowed_params().
  Return type : Array - list of common parameters
  Exceptions  : none
  Caller      : general
 
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public DBAdaptor Bio::EnsEMBL::Utils::ConversionSupport::get_database ( )
  Arg[1]      : String $database - the type of database to connect to
                (eg core, otter)
  Arg[2]      : (optional) String $prefix - the prefix used for retrieving the
                connection settings from the configuration
  Example     : my $db = $support->get_database('core');
  Description : Connects to the database specified.
  Return type : DBAdaptor of the appropriate type
  Exceptions  : thrown if asking for unknown database
  Caller      : general
 
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public DBI Bio::EnsEMBL::Utils::ConversionSupport::get_dbconnection ( )
  Arg[1]      : (optional) String $prefix - the prefix used for retrieving the
                connection settings from the configuration
  Example     : my $dbh = $self->get_dbconnection;
  Description : Connects to the database server specified. You don't have to
                specify a database name (this is useful for running commands
                like $dbh->do('show databases')).
  Return type : DBI database handle
  Exceptions  : thrown if connection fails
  Caller      : general
  Status      : At Risk
 
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public Hashref Bio::EnsEMBL::Utils::ConversionSupport::get_ensembl_chr_mapping ( )
  Arg[1]      : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Arg[2]      : (optional) String $version - coord_system version
  Example     : my $ensembl_mapping = $support->get_ensembl_chr_mapping($dba);
  Description : Gets a mapping between Vega chromosome names and their
                equivalent Ensembl chromosomes. Works with non-reference chromosomes
  Return type : Hashref - Vega name => Ensembl name
  Exceptions  : thrown if not passing a Bio::EnsEMBL::DBSQL::DBAdaptor
  Caller      : general
 
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public Array Bio::EnsEMBL::Utils::ConversionSupport::get_loutre_params ( )
  Arg         : (optional) return a list to parse or not
  Example     : $support->parse_extra_options($support->get_loutre_params('parse'))
  Description : Returns a list of commonly used loutre db parameters - parse option is
                simply used to distinguish between reporting and parsing parameters
  Return type : Array - list of common parameters
  Exceptions  : none
  Caller      : general
 
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public Arrayref Bio::EnsEMBL::Utils::ConversionSupport::get_non_hidden_slice_names ( )
  Arg[1]      : B::E::SliceAdaptor
  Arg[2]      : B::E::AttributeAdaptor
  Arg[3]      : string $coord_system_name (optional) - 'chromosome' by default
  Arg[4]      : string $coord_system_version (optional) - 'otter' by default
  Example     : $chrom_names = $support->get_non_hidden_slice_names($sa,$aa);
  Description : retrieve names of all slices from a loutre database that don't have a hidden attribute.
                Doesn't retrieve non-reference slices
  Return type : arrayref of names of all non-hidden slices
  Caller      : general
  Status      : stable
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::get_species_scientific_name ( )
  Arg[1]      : Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Example     : my $species = $support->get_species_scientific_name($dba);
  Description : Retrieves the species scientific name (Genus species) from the
                meta table
  Return type : String - species scientific name
  Exceptions  : thrown if species name can not be determined from db
  Caller      : general
 
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public Int Bio::EnsEMBL::Utils::ConversionSupport::get_taxonomy_id ( )
  Arg[1]      : Bio::EnsEMBL::DBSQL::DBAdaptor $dba
  Example     : my $sid = $support->get_taxonony_id($dba);
  Description : Retrieves the taxononmy ID from the meta table
  Return type : Int - the taxonomy ID
  Exceptions  : thrown if no taxonomy ID is found in the database
  Caller      : general
 
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public Arrayref Bio::EnsEMBL::Utils::ConversionSupport::get_unique_genes ( )
  Arg[1]      : B::E::Slice
  Arg[2]      : B::E::DBAdaptor (optional, if you don't supply one then the *first* one you generated is returned, which may or may not be what you want!)
  Example     : $genes = $support->get_unique_genes($slice,$dba);
  Description : Retrieve genes that are only on the slice itself - used for human where assembly patches
                are in the assembly_exception table. Needs the PATCHes to have 'non_ref' seq_region_attributes.
  Return type : arrayref of genes
  Caller      : general
  Status      : stable
 
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public Arrayref Bio::EnsEMBL::Utils::ConversionSupport::get_wanted_chromosomes ( )
  Arg[1]      : B::E::SliceAdaptor
  Arg[2]      : B::E::AttributeAdaptor
  Arg[3]      : string $coord_system_name (optional) - 'chromosome' by default
  Arg[4]      : string $coord_system_version (optional) - 'otter' by default
  Example     : $chr_names = $support->get_wanted_chromosomes($laa,$lsa);
  Description : retrieve names of slices from a lutra database that are ready for dumping to Vega.
                Deals with list of names to ignore (ignore_chr = LIST)
  Return type : arrayref of slices
  Caller      : general
  Status      : stable
 
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public Filehandle Bio::EnsEMBL::Utils::ConversionSupport::init_log ( )
  Example     : $support->init_log;
  Description : Opens a filehandle to the logfile and prints some header
                information to this file. This includes script name, date, user
                running the script and parameters the script will be running
                with.
  Return type : Filehandle - the log filehandle
  Exceptions  : none
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::list_all_params ( )
  Example     : print LOG $support->list_all_params;
  Description : prints a table of the parameters used in the script
  Return type : String - the table to print
  Exceptions  : none
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::list_or_file ( )
  Arg[1]      : Name of parameter to parse
  Example     : $support->list_or_file('gene');
  Description : Determines whether a parameter holds a list or it is a filename
                to read the list entries from.
  Return type : true on success
  Exceptions  : thrown if list file can't be opened
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::log ( )
  Arg[1]      : String $txt - the text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log('Log foo.\n', 1);
  Description : Logs a message to the filehandle initialised by calling
                $self->log_filehandle(). You can supply an indentation level
                to get nice hierarchical log messages.
  Return type : true on success
  Exceptions  : thrown when no filehandle can be obtained
  Caller      : general
 
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public void Bio::EnsEMBL::Utils::ConversionSupport::log_error ( )
  Arg[1]      : String $txt - the error text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log_error('Log foo.\n', 1);
  Description : Logs a message via $self->log and exits the script.
  Return type : none
  Exceptions  : none
  Caller      : general
 
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public Filehandle Bio::EnsEMBL::Utils::ConversionSupport::log_filehandle ( )
  Arg[1]      : (optional) String $mode - file access mode
  Example     : my $log = $support->log_filehandle;
                # print to the filehandle
                print $log 'Lets start logging...\n';
                # log via the wrapper $self->log()
                $support->log('Another log message.\n');
  Description : Returns a filehandle for logging (STDERR by default, logfile if
                set from config or commandline). You can use the filehandle
                directly to print to, or use the smart wrapper $self->log().
                Logging mode (truncate or append) can be set by passing the
                mode as an argument to log_filehandle(), or with the
                --logappend commandline option (default: truncate)
  Return type : Filehandle - the filehandle to log to
  Exceptions  : thrown if logfile can't be opened
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::log_stamped ( )
  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log_stamped('Log this stamped message.\n', 1);
  Description : Appends timestamp and memory usage to a message and logs it via
                $self->log
  Return type : TRUE on success
  Exceptions  : none
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::log_verbose ( )
  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Example     : my $log = $support->log_filehandle;
                $support->log_verbose('Log this verbose message.\n', 1);
  Description : Logs a message via $self->log if --verbose option was used
  Return type : TRUE on success, FALSE if not verbose
  Exceptions  : none
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::log_warning ( )
  Arg[1]      : String $txt - the warning text to log
  Arg[2]      : Int $indent - indentation level for log message
  Arg[3]      : Bool - add a line break before warning if true
  Example     : my $log = $support->log_filehandle;
                $support->log_warning('Log foo.\n', 1);
  Description : Logs a message via $self->log and increases the warning counter.
  Return type : true on success
  Exceptions  : none
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::mem ( )
  Example     : print "Memory usage: " . $support->mem . "\\n";
  Description : Prints the memory used by your script. Not sure about platform
                dependence of this call ...
  Return type : String - memory usage
  Exceptions  : none
  Caller      : general
 
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public Bio::EnsEMBL::Utils::ConversionSupport Bio::EnsEMBL::Utils::ConversionSupport::new ( )
  Arg[1]      : String $serverroot - root directory of your ensembl sandbox
  Example     : my $support = new Bio::EnsEMBL::Utils::ConversionSupport(
                                        '/path/to/ensembl');
  Description : constructor
  Return type : Bio::EnsEMBL::Utils::ConversionSupport object
  Exceptions  : thrown if no serverroot is provided
  Caller      : general
 
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public Scalar Bio::EnsEMBL::Utils::ConversionSupport::param ( )
  Arg[1]      : Parameter name
  Arg[2-N]    : (optional) List of values to set
  Example     : my $dbname = $support->param('dbname');
                $support->param('port', 3306);
                $support->param('chromosomes', 1, 6, 'X');
  Description : Getter/setter for parameters. Accepts single-value params and
                list params.
  Return type : Scalar value for single-value parameters, array of values for
                list parameters
  Exceptions  : thrown if no parameter name is supplied
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::parse_common_options ( )
  Example     : $support->parse_common_options;
  Description : This method reads options from a configuration file and parses
                some commandline options that are common to all scripts (like
                db connection settings, help, dry-run). Commandline options
                will override config file settings.
                All options will be accessible via $self->param('name').
  Return type : true on success 
  Exceptions  : thrown if configuration file can't be opened
  Caller      : general
 
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::parse_extra_options ( )
  Arg[1-N]    : option descriptors that will be passed on to Getopt::Long
  Example     : $support->parse_extra_options('string_opt=s', 'numeric_opt=n');
  Description : Parse extra commandline options by passing them on to
                Getopt::Long and storing parameters in $self->param('name).
  Return type : true on success
  Exceptions  : none (caugth by $self->error)
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::read_user_input ( )
  Arg[1]      : (optional) String $text - notification text to present to user
  Example     : my $ret = $support->read_user_input("Choose a number [1/2/3]");
                if ($ret == 1) {
                    # do something
                } elsif ($ret == 2) {
                    # do something else
                }
  Description : If running interactively, the user is asked for input.
  Return type : String - user's input
  Exceptions  : none
  Caller      : general
 
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public void Bio::EnsEMBL::Utils::ConversionSupport::remove_vega_params ( )
  Example     : $support->remove_vega_params;
  Description : Removes Vega db conection parameters. Usefull to avoid clutter in log files when
                working exclusively with loutre
  Return type : none
  Exceptions  : none
  Caller      : general
 
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public String Bio::EnsEMBL::Utils::ConversionSupport::serverroot ( )
  Arg[1]      : (optional) String - root directory of your ensembl sandbox
  Example     : my $serverroot = $support->serverroot;
  Description : Getter/setter for the root directory of your ensembl sandbox.
                This is set when ConversionSupport object is created, so
                usually only used as a getter.
  Return type : String - the server root directory
  Exceptions  : none
  Caller      : general
 
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public List Bio::EnsEMBL::Utils::ConversionSupport::sort_chromosomes ( )
  Arg[1]      : (optional) Hashref $chr_hashref - Hashref with chr_name as keys
  Example     : my $chr = { '6-COX' => 1, '1' => 1, 'X' => 1 };
                my @sorted = $support->sort_chromosomes($chr);
  Description : Sorts chromosomes in an intuitive way (numerically, then
                alphabetically). If no chromosome hashref is passed, it's
                retrieve by calling $self->get_chrlength()
  Return type : List - sorted chromosome names
  Exceptions  : thrown if no hashref is provided
  Caller      : general
 
Code:
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public String Bio::EnsEMBL::Utils::ConversionSupport::species ( )
  Arg[1]      : (optional) String $species - species name to set
  Example     : my $species = $support->species;
                my $url = "http://vega.sanger.ac.uk/$species/";
  Description : Getter/setter for species name (Genus_species). If not set, it's
                determined from database's meta table
  Return type : String - species name
  Exceptions  : none
  Caller      : general
 
Code:
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public Hashref Bio::EnsEMBL::Utils::ConversionSupport::split_chromosomes_by_size ( )
  Arg[1]      : (optional) Int $cutoff - the cutoff in bp between small and
                large chromosomes
  Arg[2]      : (optional) Boolean to include duplicate regions, ie PAR or not
                (default is no)
  Arg[3]      : (optional) Coordsystem version to retrieve
  Example     : my $chr_slices = $support->split_chromosomes_by_size;
                foreach my $block_size (keys %{ $chr_slices }) {
                    print "Chromosomes with blocksize $block_size: ";
                    print join(", ", map { $_->seq_region_name }
                                        @{ $chr_slices->{$block_size} });
                }
  Description : Determines block sizes for storing DensityFeatures on
                chromosomes, and return slices for each chromosome. The block
                size is determined so that you have 150 bins for the smallest
                chromosome over 5 Mb in length. For chromosomes smaller than 5
                Mb, an additional smaller block size is used to yield 150 bins
                for the overall smallest chromosome. This will result in
                reasonable resolution for small chromosomes and high
                performance for big ones. Does not return non-reference seq_regions
  Return type : Hashref (key: block size; value: Arrayref of chromosome
                Bio::EnsEMBL::Slices)
  Exceptions  : none
  Caller      : density scripts
 
Code:
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public Array_ref Bio::EnsEMBL::Utils::ConversionSupport::store_new_attribute ( )
  Arg[1]      : seq_region.seq_region_id
  Arg[2]      : attrib_type.code
  Arg[3]      : attrib_type.value
  ARG[4]      : table to update (seq_region_attribute by default)
  Example     : $support->store_new_attribute(23,name,5);
  Description : uses MySQL to store an entry (code and value) in an attribute table 
                (seq_region_attrib by default)
  Return type : array_ref
  Caller      : general
  Status      : stable
 
Code:
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public Array_ref Bio::EnsEMBL::Utils::ConversionSupport::update_attribute ( )
  Arg[1]      : seq_region.seq_region_id
  Arg[2]      : attrib_type.code
  Arg[3]      : attrib_type.value
  ARG[4]      : table to update (seq_region_attribute by default)
  Example     : $support->update_attribute(23,name,5);
  Description : uses MySQL to update an attribute table (seq_region_attrib by default)
  Return type : array_ref
  Caller      : general
  Status      : stable
 
Code:
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public Bio::EnsEMBL::Utils::ConversionSupport::user_confirm ( )
  Description :

Deprecated:
 
Code:
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public Boolean Bio::EnsEMBL::Utils::ConversionSupport::user_proceed ( )
  Arg[1]      : (optional) String $text - notification text to present to user
  Example     : # run a code snipped conditionally
                if ($support->user_proceed("Run the next code snipped?")) {
                    # run some code
                }
                # exit if requested by user
                exit unless ($support->user_proceed("Want to continue?"));
  Description : If running interactively, the user is asked if he wants to
                perform a script action. If he doesn't, this section is skipped
                and the script proceeds with the code. When running
                non-interactively, the section is run by default.
  Return type : TRUE to proceed, FALSE to skip.
  Exceptions  : none
  Caller      : general
 
Code:
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public Int Bio::EnsEMBL::Utils::ConversionSupport::warnings ( )
  Example     : print LOG "There were ".$support->warnings." warnings.\\n";
  Description : Returns the number of warnings encountered while running the
                script (the warning counter is increased by $self->log_warning).
  Return type : Int - number of warnings
  Exceptions  : none
  Caller      : general
 
Code:
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The documentation for this class was generated from the following file: