Florent Angly
and 1 contributors

NAME

bc_manage_members - Delete or rename community members

SYNOPSIS

  bc_manage_members -input_files   communities.generic              \
                    -exclude_names Cyanobacteria Eukaryot*          \
                    -name_prefix   "Root; "                         \
                    -output_prefix processed_communities

DESCRIPTION

This script reads files containing biological communities and includes, deletes merges, sorts or renames the specified communities. See Bio::Community for more information.

REQUIRED ARGUMENTS

-if <input_files>... | -input_files <input_files>...

Input file containing the communities to manipulate. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.

OPTIONAL ARGUMENTS

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Default: output_prefix.default

-np <name_prefix> | -name_prefix <name_prefix>

Prefix to add to the beginning of all member names. Default: name_prefix.default

-ns <name_suffix> | -name_suffix <name_suffix>

Suffix to add to the end of all member names. Default: name_suffix.default

-in <include_names>... | -include_names <include_names>...

If names of members are specified, only these members will be included in the output file. Member names can be specified using wildcards, which means that 'marine*2013' will match all names starting with 'marine' and finishing with '2013', while '*gut*' will match all names containing 'gut'.

-en <exclude_names>... | -exclude_names <exclude_names>...

Names of members to exclude from the output file. As with <include_names>, wildcards are supported.

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 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:

  http://bugzilla.open-bio.org/

AUTHOR - Florent Angly

Email florent.angly@gmail.com