- REQUIRED ARGUMENTS
- OPTIONAL ARGUMENTS
- AUTHOR - Florent Angly
bc_add_taxonomy - Add a taxonomic lineage to community members
bc_add_taxonomy -input_files my_communities.qiime \ -taxonomy_file taxonomy.tab \ -output_prefix my_communities_w_taxo
This script takes communities in which members have IDs reflecting their position in a taxonomic system and add the taxonomic lineage information to each member. The string 'unidentified' is given to members for which no taxonomic lineage is found.
- -if <input_files>... | -input_files <input_files>...
Input file containing the communities to manipulate. Your input file need to be in a format that makes provisions for member ID and taxonomic assignments (e.g. qiime and biom formats). Also, when providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files. Note that members must have IDs that are valid IDs in the taxonomic sytem used, or they will be labelled as 'unidentified'.
- -tf <taxonomy_file> | -taxonomy_file <taxonomy_file>
Taxonomy file giving the lineage information for this taxonomic system. This file should be in a format similar to that of Greengenes, i.e. tab-delimited with two columns: taxonomic ID and taxonomic lineage.
- -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
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