NAME

modules.pl - information about modules in BioPerl core

SYNOPSIS

modules.pl [-V|--verbose] [-c|--count] | [-l|--list] | [-u|--untested] | [-i|--info class] | [-i|--inherit | [-v|--version | [-?|-h|--help]

DESCRIPTION

This script counts, lists and provides other information about bioperl modules. It is mainly meant to be run by bioperl maintainers.

OPTIONS

Only one option is processed on each run of the script. The --verbose is an exception, it modifies the amount of output.

-V | --verbose

INACTIVE

Set this option if you want to see more verbose output. Often that will mean seeing warnings normally going into STDERR.

-c | --count

The default action if no other option is given. Gives the count of modules broken to instance ("usable"), base ( (abstract)? superclass) , interface (the "I" files) and component (used from instantiable parent) modules, in addition to total number of modules.

Note that abstract superclass in bioperl is not an enforced concept and they are not clearly indicateded in the class name.

-l | --list

Prints all the module names in alphabetical order. The output is a tab separated list of category (see above) and module name per line. The output can be processed with standard UNIX command line tools.

-u | --untested

Prints a list of instance modules which are not explicitly used by test files in t directory. Superclasess or any classes used by others are not reported, either, since their methods are assumed to be tested by subclass tests.

This method can not be improved much without running the tests!

-i | --info class

Dumps information about a class given as an argument.

-i | --inherit

Finds interface modules which inherit from an instantiable class.

Could be extended to check other bad inheritance patterns.

-s | --synopsis

Test SYNOPSIS section of bioperl modules for runnability

-v | --version

Test the VERSION of the module against the global one set in Bio::Root::Variation. Print out the different ones.

-? | -h | --help

This help text.

FEEDBACK

Mailing Lists

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

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

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

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho

Email heikki@ebi.ac.uk