Florent Angly > Bio-Community > bc_manage_samples

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NAME ^

bc_manage_samples - Include, delete, merge, sort or rename samples

SYNOPSIS ^

  bc_manage_samples -input_files   communities.generic              \
                    -exclude_names soil1                            \
                    -merge_names   freshwater2 freshwater5          \
                    -merge_names   marine*                          \
                    -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 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 also useful to arrange the communities in a specific order. Community 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>...

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

-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. As with <include_names>, wildcards are supported.

-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

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

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