Florent Angly > Bio-Community > bc_correct_mis_assignments

Download:
Bio-Community-0.001007.tar.gz

Annotate this POD

Website

View/Report Bugs
Source  

NAME ^

bc_correct_mis_assignments - Try fixing incorrect taxonomic assignments, using a reference community

SYNOPSIS ^

  bc_correct_mis_assignments -if my_communities.generic  \
                             -op my_modified_communities \
                             -cn theoretical

DESCRIPTION ^

This script reads a community file that contains reference communities. For every non-reference community in the file, find if the expected members are also found in the reference community. If not, use taxonomic information try to find which member of the reference community should be used instead.

REQUIRED ARGUMENTS ^

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

File containing the input communities: a reference community + communities for which to remove members not occuring in the reference community. 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

-rn <ref_name> | -ref_name <ref_name>

Name of the reference community. Default: ref_name.default

-nt <name_type> | -name_type <name_type>

Specify if <ref_name> represents a 'prefix', 'suffix', or the 'full' name of the reference community. Using prefix or suffix allows to have multiple communities with their respective reference community in the same input file. For example, using a suffic of '_theo', community 'sample1' is expected to have a reference community named 'sample1_theo'. Default: name_type.default

-bs <base_sep> | -base_sep <base_sep>

For the purpose of determining the name of the reference community, strip characters before or after the specified separator. For example, when using the prefix 'ref' and the separator '_', community 'sample1_rep1' and 'sample1_rep2' are expected to have a reference community named 'sample1_ref'.

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

syntax highlighting: