Florent Angly > Bio-Community-0.001000 > bc_convert_files

Download:
Bio-Community-0.001000.tar.gz

Annotate this POD

Website

View/Report Bugs
Source   Latest Release: Bio-Community-0.001007

NAME ^

bc_convert_files - Merge/split community files and convert between formats

SYNOPSIS ^

  # Format conversion
  bc_convert_files -input_files   my_communities.qiime     \
                   -output_format generic                  \
                   -output_prefix my_converted_communities

  # Merging communities
  bc_convert_files -input_files   some_communities.generic other_communities.generic \
                   -output_format generic                  \
                   -output_prefix my_converted_communities

DESCRIPTION ^

This script reads files containing biological communities and converts them to another format. It also several community files into a single one or splits a single file into multiple files with a single community in each. Incidentally, this scripts also removes communities with no members, or species with 0 counts in all communities.

REQUIRED ARGUMENTS ^

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

Input files containing the communities to convert. All files must have the same format, which can be one of generic (tab-delimited table), biom, qiime, gaas or unifrac. See Bio::Community::IO for more information on these format. Take note of the <member_identifier> option if you provide multiple input files.

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

-of <output_format> | -output_format <output_format>

File format to use for writing the output communities, e.g. generic (tab-delimited table), qiime, gaas or unifrac. Default: same as input format

-mi <member_identifier> | -member_identifier <member_identifier>

When putting communities from different files into a single file, two methods can be be used to decide if members of different communities are the same or not: 'id' or 'desc'. By default, the 'id' method is assumed: members with the same ID are considered the same. However, this may not always be true, e.g. when reading files generated by different programs. In this case, you can decide that members that have the same description are the same using the 'desc' method. Default: member_identifier.default

-sc <split_communities> | -split_communities <split_communities>

Split the input file(s) and generate one output file per community (1: on, 0: off). Default: split_communities.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

syntax highlighting: