LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

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NAME

Bio::EnsEMBL::Utils::ConversionSupport - Utility module for Vega release and schema conversion scripts

SYNOPSIS

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

DESCRIPTION

This module is a collection of common methods and provides helper functions for the Vega release and schema conversion scripts. Amongst others, it reads options from a config file, parses commandline options and does logging.

METHODS

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 on invalid loglevel
  Caller      : general

log_generic

  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

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

warning

  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_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

debug

  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

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

extract_log_identifier

  Arg[1]      : 
  Example     : 
  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

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

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

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

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

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

warning_count

  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

logfile

  Arg[1]      : 
  Example     : 
  Description : Getter and setter for the logfile
  Return type :
  Exceptions  : 
  Caller      : 
  Status      :

log_auto_id

  Arg[1]      : 
  Example     : 
  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

create_auto_logfile

  Arg[1]      : 
  Example     : 
  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      : At Risk
              : under development

logpath

  Arg[1]      : 
  Example     : 
  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

logappend

  Arg[1]      : 
  Example     : 
  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

is_component

  Arg[1]      : 
  Example     : 
  Description : 
  Return type : 
  Exceptions  : 
  Caller      : 
  Status      :

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL