exp-selection 1.0.0

No project description provided

ExP Selection

LCT gene

Requirements

• python >= 3.8
• vcftools (repository)
• space on disk (.vcf files are usually quite large)

Install

pip install exp-selection

Usage

Get data

• VCF files (e.g. 1000 Genomes Project and Phase 3, chr22)
• Panel file (e.g. 1000 Genomes Project)

Extract only SNP

You can give an .vcf or .vcf.gz file

# Gziped VCF
vcftools --gzvcf DATA.vcf.gz --remove-indels --recode --recode-INFO-all --out DATA.recode.vcf

# Plan VCF
vcftools --vcf DATA.vcf --remove-indels --recode --recode-INFO-all --out DATA.recode.vcf

Prepare data for computing

# DATA.recode.vcf a vcf from previous step
# DATA.zarr is path where zarr will be saved
exp-selection prepare DATA.recode.vcf DATA.zarr

Compute

# DATA.zarr a zarr data from previous step
# DATA.xpehh a path where xpehh will be saved
exp-selection compute DATA.zarr genotypes.panel DATA.xpehh

Plot graph

• --begin, --end (required)
  • plot boundaries
• --title (optional)
  • name of the image
• --cmap (optional)
  • color schema
  • more informations at seaborn package
• --output (optional)
  • png output path

bin/plot FILE.recode.xpehh --begin BEING --end END --title TITLE
# => TITLE.png

Example

# Download datasets
wget "ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/ALL.chr22_GRCh38.genotypes.20170504.vcf.gz" -O chr22.genotypes.vcf.gz
wget "ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel" -O genotypes.panel


# Compute files for graph
vcftools --gzvcf chr22.genotypes.vcf.gz \
         --remove-indels \
         --recode \
         --recode-INFO-all \
         --out chr22.genotypes.recode.vcf

exp-selection prepare chr22.genotypes.recode.vcf
exp-selection compute chr22.genotypes.recode.zarr genotypes.panel

# Plot heatmap
exp-selection plot chr22.genotypes.recode.xpehh --begin 50481556 --end 50486440 --title ADM2 --output adm2

# A heatmap is saved at adm2.png

Contributors

• Eda Ehler (@EdaEhler)
• Jan Pačes (@hpaces)
• Mariana Šatrová (@satrovam)
• Ondřej Moravčík (@ondra-m)

Acknowledgement

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