A simple tool built around ETE3 and BioPython's Eutils to convert from accession numbers to Taxonomy IDs and their associated lineage information.
The only 2 arguments needed are an email address, and a file of accession numbers, one per line, like so:
WP_041379885.1
WP_058588699.1
WP_105398703.1
...
usage: PYlogeny.py [-h] [-i INFILE] [-o OUTFILE] [-d DATABASE] -e EMAIL
[--version] [-v] [-s SQL] [-u]
Create a taxonomic breakdown for a list of accession numbers.
optional arguments:
-h, --help show this help message and exit
-i INFILE, --infile INFILE
A one-per-line file of accession numbers.
-o OUTFILE, --outfile OUTFILE
Output tabular file (default STDOUT).
-d DATABASE, --database DATABASE
What database to search for the accessions in (if you know it),
the script will attempt to use their format to guess otherwise.
-e EMAIL, --email EMAIL
Email to use with Eutils/Entrez.
--version show program's version number and exit
-v, --verbose Increase verbosity/logging. (-v or -vv)
-s SQL, --sql SQL Location to store the ETE3 database. Default is in ~/.etetoolkit/ .
If you specify a different location to the last instance, a
new copy of the database will have to be downloaded regardless.
-u, --update Update the local copy of the TaxID database.
(False by default, but should be done on a frequent basis).
Given an input list of accession numbers, create a table describing the taxonomic
memberships of those accession numbers.
The first time you run this program, and any time -u|--update is used, the
taxon dump will be made and an SQL database created. This takes several minutes.
$ PYlogeny.py -e email@domain.com -i file_of_accessions.txt
$ PYlogeny.py -vvu -e email@domain.com -i file_of_accessions.txt -s /path/to/taxdb -o lineages.csv
The ETE3 toolkit, BioPython, and absolutely requires python3 (and no, there is not going to be any Python2 compatability).
It is advised to use a miniconda/anaco
4CA1
nda installation, and install
them via:
$ conda install -c anaconda biopython
and
$ conda install -c etetoolkit ete3
The requirements.txt file shows the latest versions of these packages, since it was developed with these installed, but will likely work
with somewhat older versions too (untested).