API Reference

Funannotate2 provides a Python API that can be used to integrate the annotation pipeline into other tools or workflows.

Core Modules

Funannotate2 consists of several core modules:

clean: Functions for cleaning and preparing genome assemblies
predict: Functions for predicting genes in genome assemblies
annotate: Functions for functionally annotating predicted genes
search: Functions for searching sequences against various databases
utilities: Utility functions used by other modules
log: Logging functions used by other modules

Using the API

Here’s an example of how to use the Funannotate2 API to clean a genome assembly:

from funannotate2.clean import clean

# Create arguments object
class Args:
    def __init__(self):
        self.input = "genome.fasta"
        self.out = "cleaned_genome.fasta"
        self.minlen = 1000
        self.species = "Aspergillus fumigatus"
        self.strain = "Af293"
        self.header_slice = None
        self.sort = "size"
        self.cpus = 1
        self.tmpdir = None
        self.logfile = None
        self.force = False

args = Args()

# Clean the genome
clean(args)

Here’s an example of how to use the Funannotate2 API to predict genes:

from funannotate2.predict import predict

# Create arguments object
class Args:
    def __init__(self):
        self.input = "cleaned_genome.fasta"
        self.out = "predict_results"
        self.species = "Aspergillus fumigatus"
        self.strain = "Af293"
        self.protein_evidence = ["proteins.fasta"]
        self.transcript_evidence = ["transcripts.fasta"]
        self.augustus_species = "aspergillus_fumigatus"
        self.genemark_mode = "ES"
        self.busco_db = "fungi"
        self.busco_seed_species = None
        self.min_intron_len = 10
        self.max_intron_len = 3000
        self.min_protein_len = 50
        self.cpus = 1
        self.tmpdir = None
        self.logfile = None
        self.force = False

args = Args()

# Predict genes
predict(args)

Here’s an example of how to use the Funannotate2 API to functionally annotate predicted genes:

from funannotate2.annotate import annotate

# Create arguments object
class Args:
    def __init__(self):
        self.gff3 = "predict_results/funannotate_predict.gff3"
        self.fasta = "cleaned_genome.fasta"
        self.out = "annotate_results"
        self.species = "Aspergillus fumigatus"
        self.strain = "Af293"
        self.pfam = True
        self.dbcan = True
        self.merops = True
        self.swissprot = True
        self.busco = True
        self.busco_db = "fungi"
        self.cpus = 1
        self.tmpdir = None
        self.logfile = None
        self.force = False

args = Args()

# Annotate genes
annotate(args)