Genetics with Numpy
git clone https://github.com/oxfordmmm/gumpy
cd gumpy
pip install .
https://oxfordmmm.github.io/gumpy/
A suite of tests can be run from a terminal:
python -m pytest --cov=gumpy -vv
Genome objects can be created by passing a filename of a genbank file
from gumpy import Genome
g = Genome("filename.gbk")
VCFFile objects can be created by passing a filename of a vcf file
from gumpy import VCFFile
vcf = VCFFile("filename.vcf")
The mutations defined in a vcf file can be applied to a reference genome to produce a new Genome object containing the changes detailed in the vcf.
If a contig is set within the vcf, the length of the contig should match the length of the genome. Otherwise, if the vcf details changes within the genome range, they will be made.
from gumpy import Genome, VCFFile
reference_genome = Genome("reference.gbk")
vcf = VCFFile("filename.vcf")
resultant_genome = reference_genome + vcf
There are two different methods for comparing changes. One can quickly check for changes which are caused by a given VCF file. The other can check for changes between two genome. The latter is therefore suited best for comparisons in which either both genomes are mutated, or the VCF file(s) are not available. The former is best suited for cases where changes caused by a VCF want to be determined, but finding gene-level differences will require rebuilding the Gene objects, which can be time consuming.
Two genomes of the same length can be easily compared, including equality and changes between the two. Best suited to cases where two mutated genomes are to be compared.
from gumpy import Genome, GenomeDifference
g1 = Genome("filename1.gbk")
g2 = Genome("filename2.gbk")
diff = g2 - g1 #Genome.difference returns a GenomeDifference object
print(diff.snp_distance) #SNP distance between the two genomes
print(diff.variants) #Array of variants (SNPs/INDELs) of the differences between g2 and g1
When a Genome object is instanciated, it is populated with Gene objects for each gene detailed in the genbank file.
These genes can also be compared.
Gene differences can be found through direct comparison of Gene objects, or systematically through the gene_differences() method of GenomeDifference.
from gumpy import Genome, Gene
g1 = Genome("filename1.gbk")
g2 = Genome("filename2.gbk")
#Get the Gene objects for the gene "gene1_name" from both Genomes
g1_gene1 = g1.build_gene["gene1_name"]
g2_gene1 = g2.build_gene["gene1_name"]
g1_gene1 == g2_gene1 #Equality check of the two genes
diff= g1_gene1 - g2_gene1 #Returns a GeneDifference object
diff.mutations #List of mutations in GARC describing the variation between the two genes
Due to how long it takes to create a Genome object, it may be beneficial to save the object to disk. The reccomendation is to utilise the pickle module to do so, but due to the security implications of this, do so at your own risk! An example is below:
import pickle
import gumpy
#Load genome
g = gumpy.Genome("filename.gbk")
#Save genome
pickle.dump(g, open("filename.pkl", "wb"))
#Load genome
g2 = pickle.load(open("filename.pkl", "rb"))
g == g2 #True