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To get taxonomy ranks information with ETE3 Python3 module (http://etetoolkit.org/).
This program was from MitoZ and is still part of MitoZ (https://github.com/linzhi2013/MitoZ), so please cite the publication below if this program is helpful for you, thanks!
- Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
You can install this program via pip3 or conda or mammba (https://mamba.readthedocs.io/en/latest/) command.
$ conda install taxonomy_ranks
# or
$ mamba install taxonomy_ranksMake sure your pip3 is from Python3
$ which pip
/Users/mengguanliang/soft/miniconda3/bin/pip
then type
$ pip install taxonomy_ranks
There will be a command taxaranks created under the same directory where your pip command located.
If you want to learn more about Python3 and pip, please refer to https://www.python.org/ and https://docs.python.org/3/tutorial/venv.html?highlight=pip.
If your have MitoZ >= 3.5-beta-1 installed, you actually already have this program:
$ mitoz-tools taxonomy_ranks -h
See https://github.com/linzhi2013/MitoZ/wiki/The-%27mitoz-tools-taxonomy_ranks%27-command
$ taxaranks
usage: taxaranks [-h] [-i <file>] [-o <file>] [-t] [-v]
To get the lineage information of input taxid, species name, or higher ranks
(e.g., Family, Order) with ETE3 package.
The ete3 package will automatically download the NCBI Taxonomy database during
the first time using of this program.
Please be informed:
(1) A rank name may have more than one taxids, e.g., Pieris can means:
Pieris <butterfly> and Pieris <angiosperm>. I will search the lineages for
both of them.
(2) When you give a species name, if I can not find the taxid for the species
name, I will try to search the first word (Genus).
(3) Any input without result found will be output in outfile.err ('-o' option).
optional arguments:
-h, --help show this help message and exit
-i <file> A file can be a list of ncbi taxa id or species names (or higher
ranks, e.g. Family, Order), or a mixture of them.
-o <file> outfile
-t Also print out the taxid for each rank
-e Also print out the records without lineage information found to the '-o <file>'
-v verbose output
The -i <file> file can be a list of ncbi taxa id or species names (or higher ranks, e.g. Family, Order), or a mixture of them.
ETE3 package will automatically download the NCBI Taxonomy database during the first time using of this program.
Once the NCBI Taxonomy database has been installed, there is no need to connect to the network any more, unless you want to update the database after a period of time, for this case, please go to http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html for more details.
A taxa_name may have more than one potential_taxid.
from taxonomy_ranks import TaxonomyRanks
taxa_name = 'homo sapiens'
rank_taxon = TaxonomyRanks(taxa_name)
rank_taxon.get_lineage_taxids_and_taxanames()
ranks = ('user_taxa', 'taxa_searched', 'superkingdom', 'kingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'genus', 'subgenus', 'species')
# If you don't want the results of so many ranks, just simplify the 'ranks' tupe, e.g.
# ranks = ('user_taxa', 'taxa_searched', 'superkingdom', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species')
# The rank without a value found in the database will have the default vale 'NA'.
for potential_taxid in rank_taxon.lineages:
for rank in ranks:
if rank in ('user_taxa', 'taxa_searched'):
taxon = rank_taxon.lineages[potential_taxid][rank]
print(potential_taxid, rank, taxon, sep='\t')
else:
taxon, taxid_of_taxon = rank_taxon.lineages[potential_taxid][rank]
print(potential_taxid, rank, taxon, taxid_of_taxon, sep='\t')
# the outputs are:
9606 user_taxa homo sapiens
9606 taxa_searched homo sapiens
9606 superkingdom Eukaryota 2759
9606 kingdom Metazoa 33208
9606 superphylum NA NA
9606 phylum Chordata 7711
9606 subphylum Craniata 89593
9606 superclass Sarcopterygii 8287
9606 class Mammalia 40674
9606 subclass NA NA
9606 superorder Euarchontoglires 314146
9606 order Primates 9443
9606 suborder Haplorrhini 376913
9606 superfamily Hominoidea 314295
9606 family Hominidae 9604
9606 subfamily Homininae 207598
9606 genus Homo 9605
9606 subgenus NA NA
9606 species Homo sapiens 9606
# In the above, the taxid 9606 is for homo sapiens
# while each rank has its own taxid, e.g. 2759 is for Eukaryota.run
$ taxaranks -i test.taxa -o test.taxa.tsv
Input file test.taxacontent:
Spodoptera litura
Pieris rapae
Locusta migratoria
Frankliniella occidentalis
Marsupenaeus japonicus
Penaeus monodon
Result file test.taxa.tsv content:
user_taxa taxa_searched superkingdom kingdom superphylum phylum subphylum superclass class subclass superorder order suborder superfamily family subfamily genus subgenus species
Spodoptera litura Spodoptera litura Eukaryota Metazoa NA Arthropoda Hexapoda NA Insecta Pterygota Amphiesmenoptera Lepidoptera Glossata Noctuoidea Noctuidae Amphipyrinae Spodoptera NA Spodoptera litura
Pieris rapae Pieris rapae Eukaryota Metazoa NA Arthropoda Hexapoda NA Insecta Pterygota Amphiesmenoptera Lepidoptera Glossata Papilionoidea Pieridae Pierinae Pieris NA Pieris rapae
Locusta migratoria Locusta migratoria Eukaryota Metazoa NA Arthropoda Hexapoda NA Insecta Pterygota NA Orthoptera Caelifera Acridoidea Acrididae Oedipodinae Locusta NA Locusta migratoria
Frankliniella occidentalis Frankliniella occidentalis Eukaryota Metazoa NA Arthropoda Hexapoda NA Insecta Pterygota NA Thysanoptera Terebrantia Thripoidea Thripidae Thripinae Frankliniella NA Frankliniella occidentalis
Marsupenaeus japonicus Marsupenaeus japonicus Eukaryota Metazoa NA Arthropoda Crustacea Multicrustacea Malacostraca Eumalacostraca Eucarida Decapoda Dendrobranchiata Penaeoidea Penaeidae NA Penaeus NA Penaeus japonicus
Penaeus monodon Penaeus monodon Eukaryota Metazoa NA Arthropoda Crustacea Multicrustacea Malacostraca Eumalacostraca Eucarida Decapoda Dendrobranchiata Penaeoidea Penaeidae NA Penaeus NA Penaeus monodon
With the '-t' optioin,
$ taxaranks -i test.taxa -o test.taxa.tsv -t
Result file test.taxa.tsv will be:
user_taxa taxa_searched superkingdom superkingdom_taxid kingdom kingdom_taxid superphylum superphylum_taxid phylum phylum_taxid subphylum subphylum_taxid superclass superclass_taxid class class_taxid subclass subclass_taxid superorder superorder_taxid order order_taxid suborder suborder_taxid superfamily superfamily_taxid family family_taxid subfamily subfamily_taxid genus genus_taxid subgenus subgenus_taxid species species_taxid
Spodoptera litura Spodoptera litura Eukaryota 2759 Metazoa 33208 NA NA Arthropoda 6656 Hexapoda 6960 NA NA Insecta 50557 Pterygota 7496 Amphiesmenoptera 85604 Lepidoptera 7088 Glossata 41191 Noctuoidea 37570 Noctuidae 7100 Amphipyrinae 95182 Spodoptera 7106 NA NA Spodoptera litura 69820
Pieris rapae Pieris rapae Eukaryota 2759 Metazoa 33208 NA NA Arthropoda 6656 Hexapoda 6960 NA NA Insecta 50557 Pterygota 7496 Amphiesmenoptera 85604 Lepidoptera 7088 Glossata 41191 Papilionoidea 37572 Pieridae 7114 Pierinae 42449 Pieris 7115 NA NA Pieris rapae 64459
Locusta migratoria Locusta migratoria Eukaryota 2759 Metazoa 33208 NA NA Arthropoda 6656 Hexapoda 6960 NA NA Insecta 50557 Pterygota 7496 NA NA Orthoptera 6993 Caelifera 7001 Acridoidea 92621 Acrididae 7002 Oedipodinae 27549 Locusta 7003 NA NA Locusta migratoria 7004
Frankliniella occidentalis Frankliniella occidentalis Eukaryota 2759 Metazoa 33208 NA NA Arthropoda 6656 Hexapoda 6960 NA NA Insecta 50557 Pterygota 7496 NA NA Thysanoptera 30262 Terebrantia 38130 Thripoidea 45049 Thripidae 45053 Thripinae 153976 Frankliniella 45059 NA NA Frankliniella occidentalis 133901
Marsupenaeus japonicus Marsupenaeus japonicus Eukaryota 2759 Metazoa 33208 NA NA Arthropoda 6656 Crustacea 6657 Multicrustacea 2172821 Malacostraca 6681 Eumalacostraca 72041 Eucarida 6682 Decapoda 6683 Dendrobranchiata 6684 Penaeoidea 111520 Penaeidae 6685 NA NA Penaeus 133894 NA NA Penaeus japonicus 27405
Penaeus monodon Penaeus monodon Eukaryota 2759 Metazoa 33208 NA NA Arthropoda 6656 Crustacea 6657 Multicrustacea 2172821 Malacostraca 6681 Eumalacostraca 72041 Eucarida 6682 Decapoda 6683 Dendrobranchiata 6684 Penaeoidea 111520 Penaeidae 6685 NA NA Penaeus 133894 NA NA Penaeus monodon 6687
Warning
The reason for providing the two columns (user_taxa and taxa_searched) are,
sometimes a user input taxon may correspond to multiple NCBI taxa (probably belonging to different clades). When this happens, the lineage for all each taxon will be output, you MUST check this carefully!
If you have a lot of taxa or taxon ids to search, it could be a bit slow. For this case, please refer to #1 (Thanks to @HuoJnx !).
I have copied that code snippet to the file parallelize_taxon.sh. You can download the file to your sever, and then
sh parallelize_taxon.sh <file_list_of_ncbi_taxa_id_or_species_names>
It assumes that your server has the parallel command installed (https://anaconda.org/conda-forge/parallel).
Your HOME directory runs out of space when downloading and installing the NCBI Taxonomy database during the first time using of this program.
The error message can be:
sqlite3.OperationalEoor: disk I/O error
This is caused by ete3 which will create a directory ~/.etetoolkit to store the databse (ca. 500M), however, your HOME directory does not have enough space left.
Solutions:
The solution is obvious.
-
create a directory somewhere else that have enough space left:
$ mkdir /other/place/myetetoolkit -
remove the directory
~/.etetoolkitcreated byete3:$ rm -rf ~/.etetoolkit -
link your new directory to the HOME directory:
$ ln -s /other/place/myetetoolkit ~/.etetoolkit -
run the program again:
$ taxaranks my_taxonomy_list outfile
This way, ete3 should work as expected.
For more details, refer to http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html.
-
open a console, and type
$ python3You will enter the Python3 command line status.
-
excute following commands in Python3
>from ete3 import NCBITaxa >ncbi = NCBITaxa() >ncbi.update_taxonomy_database()
You can also manually download the database from ncbi:
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz > ncbi.update_taxonomy_database(taxdump_file='taxdump.tar.gz')
- Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
Besides, since taxonomy-ranks makes use of the ete3 toolkit, you should also cite it if you use taxonomy-ranks in your publications.
- ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; https://doi.org/10.1093/molbev/msw046
Please go to http://etetoolkit.org/ for more details.
Guanliang MENG.
linzhi2012<MitoZ>gmail<MitoZ>com