bc_convert_files - Merge/split community files and convert between formats
# 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
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.
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.
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
File format to use for writing the output communities, e.g. generic (tab-delimited table), qiime, gaas or unifrac. Default: same as input format
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
Split the input file(s) and generate one output file per community (1: on, 0: off). Default: split_communities.default
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