- REQUIRED ARGUMENTS
- OPTIONAL ARGUMENTS
- AUTHOR - Florent Angly
bc_convert_ids - Convert member ID from member attribute or file
bc_convert_ids -input_files my_communities.generic \ -output_prefix my_converted_communities \ -member_attr desc
bc_convert_ids -input_files my_communities.generic \ -output_prefix my_converted_communities \ -cluster_file gg_99_otu_map.txt
bc_convert_ids -input_files my_communities.generic \ -output_prefix my_converted_communities \ -blast_file blastn_res.tab
bc_convert_ids -input_files my_communities.generic \ -output_prefix my_converted_communities \ -taxassign_file rep_set_tax_assignments.txt
This script converts the ID of members given a metacommunity based on another member attribute, such as its description, or based on IDs provided in a file. This file can be a Greengenes OTU cluster file, a BLAST file, or a QIIME taxonomic assignment file.
- -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.
- -ma <member_attr> | -member_attr <member_attr>
Replace member ID by the value of another member attribute, e.g. the member's description field ('desc'). Replacing a member's ID by its description is useful when importing data from formats that do not explicitly represent member ID, e.g. from 'generic' to 'qiime'.
- -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).
- -bf <blast_file> | -blast_file <blast_file>
The tab-delimited BLAST file that defines the best similarity. This type of file generally has 12 columns and the first two should contain OTU ID and the ID of sequence with the best similarity. For example:
OTU_4 JN647692.1.1869 99.6 250 1 0 1 250 1 250 * * OTU_12 655879 94.4 250 14 0 1 250 1 250 * *
Note that this script expects high-quality similarity results and that only the first similarity assigned to a member is kept.
- -tf <taxassign_file> | -taxassign_file <taxassign_file>
The tab-delimited file that defines the OTU taxonomic assignments. 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.
- -cm <conversion_method> | -conversion_method <conversion_method>
Choose to either 'replace' the existing ID, 'prepend' in front of it, or 'append' after it. Default: conversion_method.default
- -cs <conversion_separator> | -conversion_separator <conversion_separator>
Set the string that will be used to construct the ID when using the 'append' or 'prepend' conversion method. Default: conversion_separator.default
- -op <output_prefix> | -output_prefix <output_prefix>
Path and prefix for the output files. Default: output_prefix.default
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