Florent Angly > Bio-Community-0.001000 > bc_use_repr_id

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NAME ^

bc_use_repr_id - Replace member ID by that of their OTU cluster or taxonomic representative

SYNOPSIS ^

  bc_use_repr_id -input_files   my_communities.generic   \
                 -output_prefix my_converted_communities \
                 -cluster_file  gg_99_otu_map.txt

or

  bc_use_repr_id -input_files    my_communities.generic   \
                 -output_prefix  my_converted_communities \
                 -taxassign_file rep_set_tax_assignments.txt

DESCRIPTION ^

This script reads a file containing biological communities and a file of OTU clusters (or taxonomic assignments) and replace the ID of the members in the communities by the ID of the representative cluster sequence (or by the ID of the taxonomic representative).

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 ^

-cf <cluster_file> | -cluster_file <cluster_file>

The tab-delimited file that defines the OTU clusters. The columns are: OTU ID, ID of the representative sequence, IDs of the other sequences in the OTU. For example:

 0      367523
 1      187144
 2      544886  544649
 3      310669
 4      355095  310677  347705  563209 

The OTU files distributed by Greengenes use this format (e.g., 99_otu_map.txt).

-tf <taxassign_file> | -taxassign_file <taxassign_file>

The tab-delimited file that defines the OTU taxonomic assignemts. The first four columns (out of 12) should be: OTU ID, taxonomic string, E-value, taxonomic ID. For example:

345 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__acnes 5e-138 1042485 95.67 300 13 0 1 300 878 579 346 k__Bacteria; p__Firmicutes; c__Bacilli; o__; f__; g__; s__ 8e-134 1064834 99.59 245 1 0 1 245 909 665 347 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__ 2e-103 959954 98.99 198 2 0 103 300 718 521

The taxonomic assignment files generated by QIIME (rep_set_tax_assignments.txt) follow this format.

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. 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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