bc_use_repr_id - Replace member ID by that of their OTU cluster or taxonomic representative
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
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).
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.
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).
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.
Path and prefix for the output files. Default: output_prefix.default
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
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.
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/
Email florent.angly@gmail.com
To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.