# taxon-utils - Taxonomy Utilities¶

## Overview¶

The script contains commands used to access functionality related to taxonomy, without the need to write ad-hoc code for functionality that can be part of a workflow. One example is access to the the last common ancestor function contained in the mgkit.taxon.

### Last Common Ancestor (lca and lca_line)¶

These commands expose the functionality of last_common_ancestor_multiple(), making it accessible via the command line. They differ in the input file format and the choice of output files.

the lca command can be used to define the last common ancestor of contigs from the annotation in a GFF file. The command uses the taxon_ids from all annotations belonging to a contig/sequence, if they have a bitscore higher or equal to the one passed (50 by default). The default output of the command is a tab separated file where the first column is the contig/sequence name, the taxon_id of the last common ancestor, its scientific/common name and its lineage.

For example:

contig_21   172788  uncultured phototrophic eukaryote   cellular organisms,environmental samples


If the -r is used, by passing the fasta file containing the nucleotide sequences the output file is a GFF where for each an annotation for the full contig length contains the same information of the tab separated file format.

The lca_line command accept as input a file where each line consist of a list of taxon_ids. The separator for the list can be changed and it defaults to TAB. The last common ancestor for all taxa on a line is searched. The ouput of this command is the same as the tab separated file of the lca command, with the difference that instead of the first column, which in this command becames a list of all taxon_ids that were used to find the last common ancestor for that line. The list of taxon_ids is separated by semicolon “;”.

Note

Both also accept the -n option, to report the config/line and the taxon_ids that had no common ancestors. These are treated as errors and do not appear in the output file.

#### Krona Output¶

New in version 0.3.0.

The lca command supports the writing of a file compatible with Krona. The output file can be used with the ktImportText/ImportText.pl script included with KronaTools. Specifically, the output from taxon_utils will be a file with all the lineages found (tab separated), that can be used with:

$ktImportText -q taxon_utils_ouput  Note the use of -q to make the script count the lineages. Sequences with no LCA found will be marked as No LCA in the graph, the -n is not required. Note Please note that the output won’t include any sequence that didn’t have a hit with the software used. If that’s important, the -kt option can be used to add a number of Unknown lines at the end, to read the total supplied. ### Filter by Taxon¶ The filter command of this script allows to filter a GFF file using the taxon_id attribute to include only some annotations, or exclude some. The filter is based on the mgkit.taxon.is_ancestor function, and the mgkit.filter.taxon.filter_taxon_by_id_list. It can also filter a table (tab separated values) when the first element is an ID and the second is a taxon_id. An example of a table of this sort is the output of the download-ncbi-taxa.sh and download-uniprot-taxa.sh, where each accession of a database is associated to a taxon_id. Multiple taxon_id can be passed, either for inclusion or exclusion. If both exclusion and inclusion is used, the first check is on the inclusion and then on the exclusion. In alternative to passing taxon_id, taxon_names can be passed, with values such as ‘cellular organisms’ that needs to be quoted. Example: $ taxon-utils filter -i 2 -in archaea -en prevotella -t taxonomy.pickle in.gff out.gff


Which will keep only line that are from Bacteria (taxon_id=2) and exclude those from the genus Prevotella. It will be also include Archaea.

Warning

Annotations with no taxon_id are not included in the output of both filters

### Convert Taxa Tables to HDF5¶

The advantage is a faster lookup of the IDs. The other is a smaller memory footprint when a great number of annotations are kept in memory.

### Changes¶

Changed in version 0.3.4: changed interface and behaviour for filter, also now can filter tables; lca has changed the interface and allows the output of a 2 column table

Changed in version 0.3.1: added to_hdf command

Changed in version 0.3.1: added -j option to lca, which outputs a JSON file with the LCA results

Changed in version 0.3.0: added -k and -kt options for Krona output, lineage now includes the LCA also added -a option to select between lineages with only ranked taxa. Now it defaults to all components.

Changed in version 0.2.6: added feat-type option to lca command, added phylum output to nolca

New in version 0.2.5.

## Options¶

### taxon-utils¶

Main function

taxon-utils [OPTIONS] COMMAND [ARGS]...


Options

--version

Show the version and exit.

--cite

#### filter¶

Filter a GFF file or a table based on taxonomy

taxon-utils filter [OPTIONS] [INPUT_FILE] [OUTPUT_FILE]


Options

-v, --verbose
-p, --table
-t, --taxonomy <taxonomy>

Taxonomy file [required]

-i, --include-taxon-id <include_taxon_id>

Include only taxon_ids

-in, --include-taxon-name <include_taxon_name>

Include only taxon_names

-e, --exclude-taxon-id <exclude_taxon_id>

Exclude taxon_ids

-en, --exclude-taxon-name <exclude_taxon_name>

Exclude taxon_names

Arguments

INPUT_FILE

Optional argument

OUTPUT_FILE

Optional argument

#### lca¶

Finds the last common ancestor for each sequence in a GFF file

taxon-utils lca [OPTIONS] [GFF_FILE] [OUTPUT_FILE]


Options

-v, --verbose
-t, --taxonomy <taxonomy>

Taxonomy file [required]

-n, --no-lca <no_lca>

File to which write records with no LCA

-a, --only-ranked

If set, only taxa that have a rank will be used in the lineageself. This is not advised for lineages such as Viruses, where the top levels have no rank

-b, --bitscore <bitscore>

Minimum bitscore accepted [default: 0]

-m, --rename

Emulates BLAST behaviour for headers (keep left of first space)

-s, --sorted

If the GFF file is sorted (all of a sequence annotations are contiguos) can use less memory, sort -s -k 1,1 can be used

-ft, --feat-type <feat_type>

Feature type used if the output is a GFF (default is LCA) [default: LCA]

-r, --reference <reference>

Reference file for the GFF, if supplied a GFF file is the output

-p, --simple-table

Uses a 2 column table format (seq_id taxon_id) TAB separated

-kt, --krona-total <krona_total>

Total number of raw sequences (used to output correct percentages in Krona

-f, --out-format <out_format>

Output a file that can be read by Krona (text) [default: tab]

Arguments

GFF_FILE

Optional argument

OUTPUT_FILE

Optional argument

#### lca_line¶

Finds the last common ancestor for all IDs in a text file line

taxon-utils lca_line [OPTIONS] [INPUT_FILE] [OUTPUT_FILE]


Options

-v, --verbose
-t, --taxonomy <taxonomy>

Taxonomy file [required]

-n, --no-lca <no_lca>

File to which write records with no LCA

-a, --only-ranked

If set, only taxa that have a rank will be used in the lineageself. This is not advised for lineages such as Viruses, where the top levels have no rank

-s, --separator <separator>

separator for taxon_ids (defaults to TAB)

Arguments

INPUT_FILE

Optional argument

OUTPUT_FILE

Optional argument

#### to_hdf¶

Convert a taxa table to HDF5, with the input as tabular format, defaults to stdin. Output file, defaults to (taxa-table.hf5)

taxon-utils to_hdf [OPTIONS] [INPUT_FILE] [OUTPUT_FILE]


Options

-v, --verbose
-n, --table-name <table_name>

Name of the table/storage to use [default: taxa]

-w, --overwrite

Overwrite the file, instead of appending to it

-s, --index-size <index_size>

Maximum number of characters for the gene_id [default: 12]

-c, --chunk-size <chunk_size>

Chunk size to use when reading the input file [default: 5000000]

Arguments

INPUT_FILE

Optional argument

OUTPUT_FILE

Optional argument