mgkit.workflow.taxon_utils module¶
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.
If a fasta file is passed, the format is changed to add the number of base pairs for each contig, showing the number of bases for each taxonomic assignment. The option -kt is not needed in this case. In that case, to generate a Krona plot:
$ ktImportText taxon_utils_ouput
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.
Multiple inclusion and exclusion flags can be put:
$ taxon-utils filter -i 2 -i 2172 -t taxonomy in.gff out.gff
In particular, the inclusion flag is tested first and then the exclusion is tested. So a line like this one:
printf "TEST\t838\nTEST\t1485" | taxon-utils filter -p -t taxonomy.pickle -i 2 -i 1485 -e 838
Will produce TEST 1485, because both Prevotella (838) and Clostridium (1485) are Bacteria (2) OR Prevotella, but Prevotella must be excluded according to the exclusion option. This line also illustrate that a tab-separated file, where the second column contains taxon IDs, can be filtered. In particular it can be applied to files produced by download-ncbi-taxa.sh or download-uniprot-taxa.sh (see Download Taxonomy).
Warning
Annotations with no taxon_id are not included in the output of both filters
Convert Taxa Tables to HDF5¶
This command is used to convert the taxa tables download from Uniprot and NCBI, using the scripts mentioned in download-data, download-uniprot-taxa.sh and download-ncbi-taxa into a HDF5 file that can be used with the addtaxa command in add-gff-info - Add informations to GFF annotations.
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.
Extract taxonomy¶
This command allows to print the taxonomy in a file created with MGKit. The default behaviour is to print the scientific name, taxon_id, rank and lineage (only ranked taxa) in a tab separated file (or standard output). IDs can also be passed along with names:
taxon-utils get -i 2147 -o prevotella -i 3688 -i 1485 -o methanobrevibacter taxonomy.msgpack
INFO - mgkit.taxon: Loading taxonomy from file taxonomy.msgpack
Acholeplasma 2147 genus Bacteria;Tenericutes;Mollicutes;Acholeplasmatales;Acholeplasmataceae;Acholeplasma
Prevotella 838 genus Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella
Salicaceae 3688 family Eukaryota;Viridiplantae;Streptophyta;Magnoliopsida;Malpighiales;Salicaceae
Methanobrevibacter 2172 genus Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae;Methanobrevibacter
Clostridium 1485 genus Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium
The taxa separator can be changed from ; with -x and common names instead of scientific names can be used with the -a option.
Match names¶
Besides the option to change the column separator, it is possible to only print specific taxa (case insensitive search, but need the correct name) and print headers for the output table. A partial and fuzzy search are performed, however these are only reported, unless option -p is passed.
The lineage is printed only for the taxa requested, but all children can be included by using the -c option.
Import Taxonomy¶
The import command allows the use of taxonomies other than NCBI and write a file that can be used with other scripts. At the moment only PhyloPhlan is supported.
PhyloPhlan¶
Tested with version 3 of the script, the taxonomy file name is similar to SGB.Sep20.txt.bz2. The file contains also NCBI IDs for known taxa and those will be kept. The IDs created for non-NCBI taxa will be negative integers, to distinguish them.
Changes¶
Changed in version 0.5.7: added –only-ids -x and -a option to get command. Added import command
Changed in version 0.5.0: added get command to taxon-utils to print the taxonomy or search in it
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.
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mgkit.workflow.taxon_utils.output_taxon_line(taxonomy, taxon_id, sep='\t', use_cname=False, taxonomy_sep=';')[source]¶
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mgkit.workflow.taxon_utils.write_krona(file_handle, taxonomy, taxon_id, only_ranked, base_pairs=None)[source]¶
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mgkit.workflow.taxon_utils.write_lca_gff(file_handle, seq_id, seq, taxon_id, taxon_name, lineage, feat_type)[source]¶