A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers
GPL-3.0 License
taxdump_url
parameter of the TaxDb
class.taxid_from_name
through the fuzzy
parameter. The degree of similarity between the query and the matches can be controlled using the score_cutoff
parameter.Published by apcamargo about 1 year ago
rank_lineage
, ranked_name_lineage
, and ranked_taxid_lineage
attributes to Taxon
.Published by apcamargo almost 2 years ago
taxid_from_name
to take a list of names as input.Published by apcamargo almost 2 years ago
nodes.dmp
and names.dmp
. By @Midnighter (https://github.com/apcamargo/taxopy/pull/13).Published by apcamargo about 2 years ago
__hash__
dunder method to Taxon
to make it hashable. By @maxibor (https://github.com/apcamargo/taxopy/pull/11).Published by apcamargo about 2 years ago
__eq__
dunder method to Taxon
.Published by apcamargo about 2 years ago
setup.py
to flit
.@property
decorator).__str__
dunder method to the Taxon
class.Taxon
's __repr__
dunder method to make it display a string that resembles GTDB's lineage strings:taxon = taxopy.Taxon(9673, taxdb)
repr(taxon)
r__Riboviria;k__Orthornavirae;p__Lenarviricota;c__Leviviricetes;o__Timlovirales
parent
method to the Taxon
class:taxon = taxopy.Taxon(9673, taxdb)
parent_taxon = taxon.parent(taxdb)
print(taxon)
print(parent_taxon)
r__Riboviria;k__Orthornavirae;p__Lenarviricota;c__Leviviricetes;o__Timlovirales
r__Riboviria;k__Orthornavirae;p__Lenarviricota;c__Leviviricetes
Published by apcamargo almost 3 years ago
taxdb.oldtaxid2newtaxid
dictionary was being accessed to create a legacy_taxid
even when a merged.dmp
file was not supplied.Published by apcamargo almost 3 years ago
taxopy
tried to read the _merged_dmp
and oldtaxid2newtaxid
attributes from the TaxDb
class itself rather than an instance.Published by apcamargo about 3 years ago
merged.dmp
and legacy taxids.Published by apcamargo about 3 years ago
rank_taxid_dictionary
attribute was added to Taxon
objects.Published by apcamargo over 3 years ago
find_lca
and find_majority_vote
functions return objects of the _AggregatedTaxon
class. _AggregatedTaxon
is a subclass of Taxon
with two additional attributes: agreement
and aggregated_taxa
.Published by apcamargo over 3 years ago
Published by apcamargo almost 4 years ago
taxid_from_name
, which takes a taxon name and returns a list containing the taxonomic identifiers associated with it.nodes.dmp
and names.dmp
are already in the directory.Published by apcamargo about 4 years ago
fraction
parameter of the find_majority_vote
function to assume values less than 0.5.Published by apcamargo about 4 years ago
weights
parameter to the find_majority_vote
function.Published by apcamargo over 4 years ago
fraction
parameter to the find_majority_vote
function.Published by apcamargo over 4 years ago
find_majority_vote
tried to create a Taxon
object using None
as input.Taxon
objects as input to find_majority_vote
.Published by apcamargo over 4 years ago
find_majority_vote
function to find the most specific taxon that is shared by more than half of the lineages of a list of taxa.Published by apcamargo over 4 years ago
Initial release.