Mailing Lists¶

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs¶

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

new¶

 Usage   : $job->new(...)
 Returns : a new analysis object, 
 Args    : none (but an implementation may choose
           to add arguments representing parameters for the analysis
           program. Each key value of must have a method implemented
           for it in a subclass. A seq () method is provided here as
           this will probably be needed by all sequence analysis programs

seq¶

 Usage   : $job->seq()
 Returns : a Bio::PrimarySeqI implementing sequence object, or void
 Args    : None, or a Bio::PrimarySeqI implementing object

analysis_name¶

    Usage     : $analysis->analysis_name();
    Returns   : The analysis name
    Arguments : none

analysis_spec¶

    Usage    :  $analysis->analysis_spec();
    Returns  :  a hash reference to  a hash of analysis parameters. See
                Bio::SimpleAnalysisI for a list of recommended key values.
    Arguments:  none

clear¶

    Usage     : $analysis->clear();
    Returns   : true value on success
    Arguments : none
    Purpose   : to remove raw results from a previous analysis so that
                an analysis can be repeated with different parameters.

input_spec¶

    Usage     : $analysis->input_spec();
    Returns   : a  reference to  an array of  hashes of analysis parameters. See
                Bio::SimpleAnalysisI for a list of recommended key values.
    Arguments : none

result_spec¶

    Usage     : $analysis->result_spec();
    Returns   : a  reference to  a   hashes of resultformats. See
                Bio::SimpleAnalysisI for a list of recommended key values. 
                The key values can be used as parameters to the result() 
                method, the values provide descriptions.
    Arguments : none