Florent Angly > Bio-Community-0.001005 > bc_summarize

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NAME ^

bc_summarize - Summarize community composition

SYNOPSIS ^

  bc_summarize -input_files   my_communities.generic   \
               -output_prefix my_converted_communities

DESCRIPTION ^

This script reads a file containing biological communities and summarizes it. In practice, this means transforming community member counts into relative abundance (taking into account any weights that members could have) and merging members that have the same lineage. Other popular practices include grouping members with a low abundance together into an 'Other' group and representing the taxonomy at a higher level, such as phylum level instead of specied level. See Bio::Community::Tools::Summarizer for more information.

REQUIRED ARGUMENTS ^

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

Input file containing the communities to summarize. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.

OPTIONAL ARGUMENTS ^

-wf <weight_files>... | -weight_files <weight_files>...

Tab-delimited files containing weights to assign to the community members.

-wa <weight_assign> | -weight_assign <weight_assign>

When using a files of weights, define what to do for community members whose weight is not specified in the weight file (default: weight_assign.default):

* $num : assign to the member the arbitrary weight $num provided

* file_average : assign to the member the average weight in this file.

* community_average : assign to the member the average weight in this community.

* ancestor: go up the taxonomic lineage of the member and assign to it the weight of the first ancestor that has a weight in the weights file. Fall back to the 'community_average' method if no taxonomic information is available for this member (for example a member with no BLAST hit).

See the weight_assign() method in Bio::Community::IO for more details.

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Default: output_prefix.default

-cr <convert_relab> | -convert_relab <convert_relab>

Convert counts into relative abundances (in percentage, taking into account weights): 1 (yes), 0 (no). Default: convert_relab.default

-md <merge_dups> | -merge_dups <merge_dups>

Merge community members with the exact same lineage. Default: merge_dups.default

-td <taxo_dups> | -taxo_dups <taxo_dups>

By default, the lineage of species has to match character for character for them to be considered duplicates. When you activate this option (1:on, 0:off), their lineage is parsed and interpreted taxonomically. For example, these three members would be duplicates:

  k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria
  k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria
  k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__;f__;g__;s__

Default: taxo_dups.default

-rl <relab_lt> | -relab_lt <relab_lt>

Group community members with a relative abundance less than the specified threshold (in %) in ALL the communities into an 'Other' group. Default: relab_lt.default %

-tl <tax_level_min> [.. <tax_level_max>] | -tax_level <tax_level_min> [.. <tax_level_max>]

Group members belonging to the same taxonomic level. For the Greengenes taxonomy, level 1 represents kingdom, level 2 represents phylum, and so on, until level 7, representing the species level. Members without taxonomic information are grouped together in a member with the description 'Unknown taxonomy'. Default: none

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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