Orthologs.Blast.ComparativeGenetics

Main Comparative Genetics class.

Usage

Source

Orthologs.Blast.ComparativeGenetics(
    project,
    template=None,
    taxon_file=None,
    ref_species=None,
    post_blast=False,
    save_data=True,
    **kwargs
)

Methods

Name Description
__init__() Inherits BaseComparativeGenetics to build a file layer to the Blast workflow.
add_accession() Build an accession file after a Blastn run.
add_blast_time() Build a file that stores the amount of time for each gene to blast.
post_blast_analysis() Write duplicate, missing, and removed-gene results to Excel.

__init__()

Inherits BaseComparativeGenetics to build a file layer to the Blast workflow.

Usage

Source

__init__(
    project,
    template=None,
    taxon_file=None,
    ref_species=None,
    post_blast=False,
    save_data=True,
    **kwargs
)

This class handles all of the files before and after the Blast occurs. It also uses a building file to start where a previous blast left off.

Parameters
project

The name of the project.

template=None

A template accession file in the desired format. See the Blast README for an example.

taxon_file=None

A list of taxon ids in a text file.

ref_species=None

A reference species or organism for the blast query.

post_blast=False

A flag that triggers the post blast analysis.

save_data=True

A flag that indicates whether the data should be saved in an excel file or not.

kwargs={}
Mostly used for BaseComparativeGenetics
Returns
An API for accessing the various files used before, during, and after blasting.

add_accession()

Build an accession file after a Blastn run.

Usage

Source

add_accession(gene, organism, accession)

It finds whether or not the Blast has been interrupted or not, so that the Blast can pick up where it left off.

Parameters
gene

The gene of interest.

organism

The organism of interest.

accession
The accession of interest.
Returns

add_blast_time()

Build a file that stores the amount of time for each gene to blast.

Usage

Source

add_blast_time(gene, organism, start, end)

This method is similar to the add_accession() method.

Parameters
gene: str

The gene of interest.

organism: str

The organism of interest.

start: float

Starting time.

end: float
Ending time.

post_blast_analysis()

Write duplicate, missing, and removed-gene results to Excel.

Usage

Source

post_blast_analysis(removed_genes=None)