Florent Angly
and 1 contributors


bc_manage_members - Delete or rename community members


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


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


-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.


-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.


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AUTHOR - Florent Angly

Email florent.angly@gmail.com