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Florent Angly > Bio-Community-0.001000 > bc_manage_samples


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Source   Latest Release: Bio-Community-0.001007


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.


-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 community names. Default: name_prefix.default

-ns <name_suffix> | -name_suffix <name_suffix>

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

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

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.

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

If names of communities are specified, these communities will be excluded from the output file.

-mn <merge_names>... | -merge_names <merge_names>...

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.

-rm <renaming_method> | -renaming_method <renaming_method>

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.

Default: renaming_method.default


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.                  - General discussion  - About the mailing lists


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

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:

AUTHOR - Florent Angly ^


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