Florent Angly > Bio-Community > bc_add_taxonomy

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NAME ^

bc_add_taxonomy - Add a taxonomic lineage to community members

SYNOPSIS ^

  bc_add_taxonomy -input_files   my_communities.qiime  \
                  -taxonomy_file taxonomy.tab          \
                  -output_prefix my_communities_w_taxo

DESCRIPTION ^

This script takes communities in which members have IDs reflecting their position in a taxonomic system and add the taxonomic lineage information to each member. The string 'unidentified' is given to members for which no taxonomic lineage is found.

REQUIRED ARGUMENTS ^

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

Input file containing the communities to manipulate. Your input file need to be in a format that makes provisions for member ID and taxonomic assignments (e.g. qiime and biom formats). Also, when providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files. Note that members must have IDs that are valid IDs in the taxonomic sytem used, or they will be labelled as 'unidentified'.

-tf <taxonomy_file> | -taxonomy_file <taxonomy_file>

Taxonomy file giving the lineage information for this taxonomic system. This file should be in a format similar to that of Greengenes, i.e. tab-delimited with two columns: taxonomic ID and taxonomic lineage.

OPTIONAL ARGUMENTS ^

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Several output files will be created if the requested output format can only hold a single community. Default: output_prefix.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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