example.tax

# This is an example file of how a tax file used to provide taxon IDs for an alignment to be
# imported into the EvoNAPS database should be formatted.
#
# The file should be formatted as a csv file. with the following columns:
#   1. SEQ_NAME: The first column contains the name of the sequence EXACTLY as it appears 
#        in the alignmnet file.
#   2. TAX_ID: The second column holds the taxon ID of the sequence (according to NCBI taxonomy table).
#   3. TAX_CHECK: The third column holds an integer indicating how the taxon ID was determined. 
#       - 1 indicates that the TAX_ID was determined based on the sequence name only.
#       - 2 suggests the information was taken from an (unchecked) external source.
#       - 3 states that the information was checked manually (e.g., check publication). It is the DEFAULT value.
#       - 4 indicates highest confidence in the rovided taxon ID. The source of seqeunces is known to uploadeer 
#            or taxon ID was determined using an available accession number.
#       The third column can stay blank (3 will be assumed in this case).
#   4. Potential accession number. Can also stay blank.
#   5... Any further columns will be ignored.
#
# Lines starting with # will be ignored.
# This file is expected to have no headline. If you wish to include one, comment it out.
# SEQ_NAME,TAX_ID,TAX_CHECK,COMMENT
"Homo_sapiens_123", 9606,2,,This is a human sequence., "Another comment",,,,
"Mus_musulus_987",10090,,,This is a mouse sequence. The third column is blank (3 is assumed).
"species_NZ_JBAFXE010000000",7,4,NZ_JBAFXE010000000,This is a Azorhizobium caulinodans sequence. The taxon ID was determined using an accession number (which is also the name given to the sequence).