African Cattle Analyses

pip install ipykernel

To count base frequencies,

python cow.py filename.fasta
python Seqtest.py filename.fasta

Name		Name	Last commit message	Last commit date
Latest commit History 75 Commits
datafiles		datafiles
metadata		metadata
vcf_manip		vcf_manip
Cattle_data_exploration.ipynb		Cattle_data_exploration.ipynb
README.md		README.md
Seqtest.py		Seqtest.py
TableS2.csv		TableS2.csv
VCFtoFASTA.py		VCFtoFASTA.py
VCFtoFASTA_onebyone.py		VCFtoFASTA_onebyone.py
addition.py		addition.py
calculate_d_dplus_genomewide_cows.py		calculate_d_dplus_genomewide_cows.py
cow.py		cow.py
cowanalyzertest.py		cowanalyzertest.py
data_manipulation.sh		data_manipulation.sh
jsequence.py		jsequence.py
ncbi.sh		ncbi.sh
ndama_chrome_10.vcf		ndama_chrome_10.vcf
pseudocode.py		pseudocode.py
run_bash_python_bos_indicus-p1.sh		run_bash_python_bos_indicus-p1.sh
sequence.fasta		sequence.fasta
simulated_data_mctavish_lab.vcf		simulated_data_mctavish_lab.vcf
tester.py		tester.py
vcf_chunks.py		vcf_chunks.py
vcftofasta.sh		vcftofasta.sh

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