Predict Height

Predict height by gender and genotypes.

Usage

Prepare data

Training datasets

Specimen file as below: 5 columns (label, name, gender, height, date of birth, age)

GW7S0140C01	张三	male	176	1954-03-05	
GW7S0140C02	李四	female	170	1992-12-28	26
GW7S0140C03	王五	male	175	1957-10-01	

Genotype file as below: 4 columns (label, rs, allele1, allele2)

GW7S0140C01	rs12688220	T	T
GW7S0140C01	rs5912838	A	C
GW7S0140C01	rs137852591	C	C
GW7S0140C01	rs267606617	A	A
GW7S0140C01	rs267606619	C	C

Parse files

python parse_inputs.py -s <specimen_file> -g <genotype_file> -o <output_file> -l

Predict datasets

Genotype file as below: 3 columns (rs, allele1, allele2)

rs12688220	T	T
rs5912838	A	C
rs137852591	C	C
rs267606617	A	A
rs267606619	C	C

Parse file

python parse_inputs.py -g <genotype_file> -o <output_file> --gender=<gender>

Train and save models

Use train datasets from parsed train datasets above, will train models and save model to models(default) directory.

python train.py <tain_datesets>

Predict

Use target datasets from parsed predict datasets above, will output predicted height by model.

python predict.py <target_datasets>