ncbitaxonomy
This is a Rust crate (i.e. library) for working with a local copy of the
NCBI Taxonomy database.
The database can be downloaded (either taxdump.zip or taxdump.tar.gz) from the
NCBI Taxonomy FTP site.
Documentation for version 0.1.3 is available at crates.io.
taxonomy_filter_refseq
(new in 0.1.1)
A tool to filter a NCBI RefSeq FASTA file so that only the ancestors of a given taxon
are retained.
$ taxonomy_filter_refseq --help
taxonomy_filter_refseq 0.1.2
Peter van Heusden <pvh@sanbi.axc.za>
Filter NCBI RefSeq FASTA files by taxonomic lineage
USAGE:
taxonomy_filter_refseq [OPTIONS] <INPUT_FASTA> <TAXONOMY_DIR> <ANCESTOR_NAME> [OUTPUT_FASTA]
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-t, --tax_prefix <TAXONOMY_FILENAME_PREFIX> String to prepend to names of nodes.dmp and names.dmp
ARGS:
<INPUT_FASTA> FASTA file with RefSeq sequences
<TAXONOMY_DIR> Directory containing the NCBI taxonomy nodes.dmp and names.dmp files
<ANCESTOR_NAME> Name of ancestor to use as ancestor filter
<OUTPUT_FASTA> Output FASTA filename (or stdout if omitted)
taxonomy_filter_fastq
(new in version 0.2.0)
$ taxonomy_filter_fastq --help
taxonomy_filter_refseq 0.1.2
Peter van Heusden <pvh@sanbi.axc.za>
Filter NCBI RefSeq FASTA files by taxonomic lineage
USAGE:
taxonomy_filter_fastq [FLAGS] [OPTIONS] <INPUT_FASTQ> --ancestor_taxid <ANCESTOR_ID> --taxdir <TAXONOMY_DIR> --tax_report_filename <TAXONOMY_REPORT_FILENAME> <--centrifuge|--kraken2>
FLAGS:
-d, --output_dir Directory to deposited filtered output files in
-C, --centrifuge Filter using report from Centrifuge
-h, --help Prints help information
-K, --kraken2 Filter using report from Kraken2
-V, --version Prints version information
OPTIONS:
-A, --ancestor_taxid <ANCESTOR_ID> Name of ancestor to use as ancestor filter
-T, --taxdir <TAXONOMY_DIR>
Directory containing the NCBI taxonomy nodes.dmp and names.dmp files
-t, --tax_prefix <TAXONOMY_FILENAME_PREFIX> String to prepend to names of nodes.dmp and names.dmp
-F, --tax_report_filename <TAXONOMY_REPORT_FILENAME> Output from Kraken2 (default) or Centrifuge
ARGS:
<INPUT_FASTQ> FASTA file with RefSeq sequences
