bc_manage_samples - Include, delete, merge, sort or rename samples
bc_manage_samples -input_files communities.generic \ -exclude_names community1 \ -merge_names community2 community5 \ -merge_names community7 community8 community9 \ -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.
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.
Path and prefix for the output files. Default: output_prefix.default
Prefix to add to the beginning of all community names. Default: name_prefix.default
Suffix to add to the end of all community names. Default: name_suffix.default
If names of communities are specified, only these communities will be included in the output file, in the requested order. This is useful to sort communities.
If names of communities are specified, these communities will be excluded from the output file.
Specify the name of the communities to merge. Use this option multiple time if you need to merge multiple sets of communities. The count of the members of these communities are added.
When merging communities, specify a method to generate a name for the merged community:
* a character that will join the names of the communities to merge, e.g. '+', '_', ...
* 'first': use the name of the first community
* 'common': The largest substring common between the names, starting from the left. After this, any trailing, non-alphanumerical character is considered a separator and removed.
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