hiv-zipcode-tools

Tools for extraction and clustering of HIV zipcodes

Updated for multi sizes

Uses custom code for Needleman–Wunsch alignment of small sequences

to setup before initial use, run:

python setup.py build_ext --inplace

to make .so file using cython

Name		Name	Last commit message	Last commit date
Latest commit History 47 Commits
.gitignore		.gitignore
README.md		README.md
add-family-to-align-parse.py		add-family-to-align-parse.py
assign-insertions.py		assign-insertions.py
collapse-insertion-map.py		collapse-insertion-map.py
combine-assignment-table.py		combine-assignment-table.py
combine-ziptable-norm.py		combine-ziptable-norm.py
extract-zips-insertion-sites.py		extract-zips-insertion-sites.py
extract-zips.py		extract-zips.py
form-clusters-from-table.py		form-clusters-from-table.py
merge-quant-tables.py		merge-quant-tables.py
pairwisealign.pyx		pairwisealign.pyx
preprocess-insertion-shear-brkkpnts.py		preprocess-insertion-shear-brkkpnts.py
process-bam.py		process-bam.py
quantify-clusters.py		quantify-clusters.py
select-clusters.py		select-clusters.py
setup.py		setup.py
zipcodetools.py		zipcodetools.py

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