Florent Angly > Bio-Community-0.001000 > bc_get_info

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Source   Latest Release: Bio-Community-0.001007

NAME ^

bc_get_info - Get information about a community file

SYNOPSIS ^

  bc_get_info -input_files   my_communities.generic \
              -output_prefix my_info.txt            \
              -info_type     'members'

DESCRIPTION ^

This script reads a file containing biological communities and retrieves basic information from it, such as the names of the communities it contains and their counts, the ID of members and their description, or the file format. The information is displayed on screen unless an output prefix is provided.

REQUIRED ARGUMENTS ^

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

Input file containing the communities to process. 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 file. The output is displayed on screen if no output prefix is provided. Default: none

-it <info_type> | -info_type <info_type>

Type of information to return, either:

   'communities' for community names (in order of appearance) and their member count
   'members' for member IDs (in no specific order) and their description
   'format' for the file format

Default: info_type.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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