VCFruit

VCFruit.py makes a VCBerry Class Object

• Pulls in vcf file and makes a class called VCBerry.
• VCBerry generates the following pandas DataFrames:
  • VCBerry.snps are only SNPs.
  • VCBerry.indels are only INDELs.
  • VCBerry.monomeric are invariant sites.
• Call on VCBerry in a module via:
  • new_df = VCBerry(vcfile)
  • function_return = new_df.snps
• Other attributes of a VCBerry object:
  • VCBerry.allvars outputs a combined snp/indel DataFrame.
  • VCBerry.header provides the original vcf header for compiling a new vcf.

Modules

Papaya.ipynb : Variant Position Visualization

• Papaya is a Jupyter notebook that visualizes the position of varaints on a chromosome.
• The frequency of variants at binned positions along the chromosome is visualized with a Manhattan plot and a heat map.
• Strawberry also plots the nucleotide change frequencies across all variants.

Jackfruit.py : A Motif Module

• Jackfruit uses the JASPAR databse to identify variants within transcription factor binding sites.
• Jackfruit takes in a VCBerry.snp database and outputs a dictionary of reference and alternate TF binding motifs.
• The INDEL version of Jackfruit is in progress, named Durian.py
• ** Ideal output would be a .tsv

Strawberry.py : Population-level Variant Analysis

• Strawberry extracts the genotype of every individual for every variant.
• Strawberry then calculates the ***

Melon.py

• Annotates variants with the reference annotation.

Grapes.py

• Grapes provides variant position in a chromosome.

WaterMelon.py: Variant Annotation

• WaterMelon annotates variants with the reference annotated genome.

Lychee

LycheeMelon.py

• LycheeMelon outputs reference and alternate sequence.

Lychee.py : Variant Effect Predictor

• Lychee takes the annotated reference and alternate sequences and predicts the effect of the variant.
• Lychee maps codons to amino acids and determines synonymous versus nonsynonymous mutations based on amino acid properties.
• Lychee outputs the translated sequences and associated properties of the variants. **txt file?

Fruit_Basket.py

• Fruit Basket integrates all the VCFruit modules with the exception of Papaya.
• The output is a series of files that describe, analyze, and annotate a contributed VCF.