/usr/share/doc/ray/Documentation/Taxonomy.txt is in ray-doc 2.3.1-2build2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | Ray Communities is a set of RayPlatform-compatible plugins that adds search
capabilities to the Ray distributed k-mer storage engine.
== Ray command ==
mpiexec -n 4 Ray \
-p s1.fastq s2.fastq \
-search NCBI-Bacteria \
-with-taxonomy \
Genome-to-Taxon.tsv \
TreeOfLife-Edges.tsv \
Taxon-Names.tsv
The directory NCBI-Bacteria/ contains one fasta file per strain/species.
Each header should be like:
>gi|225853611|ref|NC_012466.1| Streptococcus pneumoniae JJA, complete genome |
The identifiers (225853611 in this example) are used to place things in the tree of life.
The mapping from gi numbers to taxonomy numbers is done using the file
Genome-to-Taxon.tsv. The taxonomy tree edges is contained in
TreeOfLife-Edges.tsv. Finally, the name of the taxons are provided in
Taxon-Names.tsv.
For the NCBI taxonomy, see Documentation/NCBI-Taxonomy.txt
== Genome-to-Taxon.tsv ==
Each line has 2 columns (tab-separated):
GenBankIdentifier taxonIdentifier
Both are integers.
== TreeOfLife-Edges.tsv format ==
Each line has 2 columns (tab-separated):
parentTaxonIdentifier childTaxonIdentifier
Both are integers.
== Taxon-Names.tsv ==
Each line has 3 columns (tab-separated):
taxonIdentifier taxonName taxonomicRank
taxonIdentifier is an integer
taxonName is a string
taxonomicRank is a string
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