oggmap.qlin module

Author: Kristian K Ullrich date: February 2025 email: ullrich@evolbio.mpg.de License: GPL-3

oggmap.qlin.add_argparse_args(parser: ArgumentParser)

This function attaches individual argument specifications to the parser.

Parameters:

parser (argparse.ArgumentParser) – An argparse.ArgumentParser.

oggmap.qlin.define_parser()

A helper function for using qlin.py via the terminal.

Returns:

An argparse.ArgumentParser.

Return type:

argparse.ArgumentParser

oggmap.qlin.get_lineage_topo(qt, ncbi=None, dbname=None)

This function returns a species lineage as a tree object for a query species given as taxID.

Parameters:

  • qt (str) – The taxID of the queried species.

  • ncbi (dict) – The NCBI taxonomic database.

  • dbname (str) – Specify taxadb.sqlite file.

Returns:

The lineage of the queried species as a Bio.Phylo.Newick.Tree.

Return type:

Bio.Phylo.Newick.Tree

Example

>>> from oggmap import qlin
>>> lineage_tree = qlin.get_lineage_topo(qt='10090',
>>>                                      dbname='taxadb.sqlite')
>>> lineage_tree
oggmap.qlin.get_oldest_common(ql, tl)

This function returns the oldest common ancestor (OCA) by comparing the lineage information of a query species and a target species.

The target species can also be a list of LCA values to find the oldest among the given LCA.

Parameters:

  • ql (list) – Query species lineage information.

  • tl (list) – Target species lineage information.

Returns:

oldest common ancestor (OCA).

Return type:

str

Example

>>> from oggmap import qlin
>>> # get query species taxonomic lineage information
>>> _, _, query_lineage, _, _, _, _, _ = qlin.get_qlin(q='Caenorhabditis elegans',
>>>                                                    dbname='taxadb.sqlite')
>>> # get target species taxonomic lineage information
>>> _, _, target_lineage, _, _, _, _, _ = qlin.get_qlin(q='Mus musculus',
>>>                                                     dbname='taxadb.sqlite')
>>> # get oldest common node
>>> qlin.get_oldest_common(ql=query_lineage, tl=target_lineage)
oggmap.qlin.get_qlin(q=None, qt=None, quiet=False, ncbi=None, dbname=None)

This function searches the NCBI taxonomic database for results matching the query name or query taxID.

Note that if the user specifies both the name and the taxID of a species, the returning result is based on the taxID.

Parameters:

  • q (str) – The name of the queried species.

  • qt (str) – The taxID of the queried species.

  • quiet (bool) – Specify if output should be quiet.

  • ncbi (dict) – The NCBI taxonomic database.

  • dbname (str) – Specify taxadb.sqlite file.

Returns:

A list of information for the queried species such as: query name, query taxID, query lineage, query lineage dictionary, query lineage zip, query lineage names, reverse query lineage, query kingdom

Return type:

list

Example

>>> from oggmap import qlin
>>> qlin.get_qlin(q='Danio rerio',
>>>               dbname='taxadb.sqlite')
oggmap.qlin.get_youngest_common(ql, tl)

This function returns the lowest common ancestor (LCA) by comparing the lineage information of a query and a target species.

Parameters:

  • ql (list) – Query species lineage information.

  • tl (list) – Target species lineage information.

Returns:

lowest common ancestor (LCA).

Return type:

str

Example

>>> from oggmap import qlin
>>> # get query species taxonomic lineage information
>>> _, _, query_lineage, _, _, _, _, _ = qlin.get_qlin(q='Caenorhabditis elegans',
>>>                                                    dbname='taxadb.sqlite')
>>> # get target species taxonomic lineage information
>>> _, _, target_lineage, _, _, _, _, _ = qlin.get_qlin(q='Mus musculus',
>>>                                                     dbname='taxadb.sqlite')
>>> # get youngest common node
>>> qlin.get_youngest_common(ql=query_lineage, tl=target_lineage)
oggmap.qlin.load_taxadb(ncbi, dbname)

Load taxadb.sqlite database or exit if neither ncbi nor dbname are provided.

Parameters:

  • ncbi – Existing ncbi dictionary, if any.

  • dbname – Path to taxadb.sqlite file.

Return type:

dict

oggmap.qlin.main()

The main function that is being called when qlin is used via the terminal.

oggmap.qlin.ncbi_get_lineage(qt, ncbi=None, dbname=None)

This function returns a species lineage for a query species given as taxID.

Parameters:

  • qt (str) – The taxID of the queried species.

  • ncbi (dict) – The NCBI taxonomic database.

  • dbname (str) – Specify taxadb.sqlite file.

Return type:

list

oggmap.qlin.ncbi_get_taxid_translator(qt_vec, ncbi=None, dbname=None)

This function returns a dictionary for a vector of taxIDs as integers.

Parameters:

  • qt_vec (list of int) – A vector of taxIDs as integers.

  • ncbi (dict) – The NCBI taxonomic database.

  • dbname (str) – Specify taxadb.sqlite file.

Return type:

dict

oggmap.qlin.traverse_postorder(clade)

Yield each clade (node) in a post-order traversal (children before parent)

Parameters:

clade (Bio.Phylo.Newick.Clade) – A Clade object from a Bio.Phylo.Newick.Tree.