Annotation surjection with Ixchel

Ixchel is a genome-graph based tool intended to aid in the conversion of annotations in graph-coordinates to linear coordinates. It is early in development and currently only has functionality designed for surjecting annotations (.graph.methyl) data for CpG sites. Currently, it only works with CpG sites, but the goal is to expand it to other types of annotations. Given the tremendous size of genomes, the steps will likely need to be run individually on a cluster.

Overview of Ixchel process

flowchart TB
    Genomegraph["Genome-graph (.GFA)"] --> IxchelPrep["1) Ixchel prepareGraphFiles"]
    IxchelPrep --> GraphFiles["Pre-computed conversion files"]
    GraphFiles --> IxchelSurject["2) Ixchel convertGraphMethylToMethylC"]
    Annotations["Annotations (.graph.methyl)"] --> IxchelSurject
    IxchelSurject --> SurjectedAnnotations["Surjected annotations (.methylC)"]
    SurjectedAnnotations --> IxchelInterpretCodes["3) Ixchel convertConversionCodes"]
    IxchelInterpretCodes --> ExpandedCodes["Expanded conversion codes"]
    
    classDef default fill:#fff,stroke:#333,stroke-width:4px,color:black;

Run Ixchel end-to-end

Ixchel requires a genome graph in GFA format. It was designed to work with graphs produced by minigraph-cactus and is compatible with the human pangenomes available here. It is run in two steps:

Prepare the graph files
Convert the graph.methyl annotations to methylC format

cd /scratch/hllab/Juan/Ixchel_Dev_Tests/VGPlayGround
srun --mem=8000 --cpus-per-task=1 -J interactive -p interactive --pty /bin/bash -l
eval $( spack load --sh python@3.7.3 )
eval $( spack load --sh py-numpy/i7mcgz4 )
eval $( spack load --sh py-jsonpickle@1.4.1 )
eval $( spack load --sh py-dill@0.3.4 )

Prepare the graph files

python3 /scratch/hllab/Juan/Ixchel/SourceCode/Ixchel.py prepareGraphFiles TestGraph.gfa

Convert GraphMethyl to MethylC

python3 /scratch/hllab/Juan/Ixchel/SourceCode/Ixchel.py convertGraphMethylToMethylC Example.CG.graph.methyl Annotations.Segments.TestGraph.gfa.pkl

Extract and interpret codes

Ixchel uses a set of codes to represent the context of segments in the graph. Context that affects how precisely the segment can be surjected to linear coordinates.

python3 /scratch/hllab/Juan/Ixchel/SourceCode/Ixchel.py convertConversionCodes Example.CG.graph.methylc

twlab / Ixchel