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Check data validity
trvinh edited this page Sep 24, 2020
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Normally all data come together with fDOG and data resulted from fdog.addTaxon or fdog.addTaxa are ready to use. However, if you manually add taxa into fDOG, you should check for their validity by running this command:
fdog.checkData [-g GENOMEDIR] [-b BLASTDIR] [-w WEIGHTDIR] [--replace] [--delete] [--concat]
GENOMEDIR, BLASTDIR and WEIGHTDIR are only needed if they are not placed in the same directory of the installed fDog.
This script will check for:
- valid folder name (must not contain PIPE, space or some other special characters)
- valid fasta file (no space/tab allowed, no special characters or numbers in the sequences, each sequence must be written in single line)
- missing annotations (all taxa present in genome_dir and blast_dir must have annotations in weight_dir)
- missing or duplicated NCBI taxonomy IDs
You will have options to process the fasta files if they are not in the right format, such as delete special characters in the sequences, or replace them with "X", or convert multi-line sequences into single-line sequences.