Setup (make sure you have python3.10)
pip install -r requirements.txt
cd hw1
python hw1.py
Input: hw1/HW1.txt
Output: hw1/HW1_ans.txt
Read Clinvar VCF
cd hw2
python hw2.py
Input: hw2/HW2_clinvar.txt
Output: hw2/hw2_clnsig.png
hw2/hw2_rs.tsv
cd hw2_2
./hw2_2.sh
Input: /localpath/a_very_big_trash.tar.gz
Output: hw2_2/answer/home.txt
, hw2_2/answer/location.txt
see week3/README.md
Some pair of sequences are mapped on the reference by blast,
and then calculate the insertion size of the pair.
Some pair should be removed if the mapping result doesn't meet some criteria.
cd hw3
python hw3.py
input: hw3/rat_sample.fa
Output: hw3/rat_sample_merge.stat.csv
see week4/README.md
cd hw4
# N50 practice
python hw4_1.py > hw4.1.txt
# Parse Result of https://github.com/metagenome-atlas/Tutorial.git and answer questions
python hw4_2.py > hw4.2.txt
input: HW4.1.txt
Tutorial/Example
Output: hw4.1.txt
HW4.2.txt
hw4.2.png
Extract the phased genotype of specific position from sam file.
cd hw5
python hw5.py
input: hw5.sam
(Not provided), ITGA2B.vcf
Output: hw5.ITGA2B.count.tsv
hw5.chr17.*.strange_case.bam
see week5/README.md
cd week5
python week5_graph.py
input: NA
Output: week5/c3.sample.c3_vg.sort.gam.gai
week5/c3.sample.c3_hisat.bam
see week6/README.md
see hw6/README.md
see final/README.md