My personal package for bioinformatics related stuff
Project description
lhc-python
This is my personal library of python classes and functions, many of them have bioinformatics applications. The library changes constantly and at a whim. If you want to use it, approach with caution.
cli
Tools with a command line interface.
These can be used from the command line after the library has been installed using python -m lhc.cli.<package_name>.
alignments
python -m lhc.cli.alignments cs_to_table
python -m lhc.cli.alignments mismatch_filter
python -m lhc.cli.alignments strand
loci
python -m lhc.cli.loci closest
python -m lhc.cli.loci deduplicate
python -m lhc.cli.loci strand
python -m lhc.cli.loci filter
python -m lhc.cli.loci flank
python -m lhc.cli.loci generate
python -m lhc.cli.loci kmer_filter
python -m lhc.cli.loci query
python -m lhc.cli.loci shear
python -m lhc.cli.loci stats
python -m lhc.cli.loci view
multiple_alignments
python -m lhc.cli.multiple_alignments align_pairwise
python -m lhc.cli.multiple_alignments call_variants
python -m lhc.cli.multiple_alignments extract
python -m lhc.cli.multiple_alignments get_consensus
python -m lhc.cli.multiple_alignments trim_gaps
sequences
python -m lhc.cli.sequences barcode_filter
python -m lhc.cli.sequences barcode_split
python -m lhc.cli.sequences extract
python -m lhc.cli.sequences filter
python -m lhc.cli.sequences interleave
python -m lhc.cli.sequences rmdup
python -m lhc.cli.sequences split
python -m lhc.cli.sequences stat
python -m lhc.cli.sequences unique
python -m lhc.cli.sequences view
variants
python -m lhc.cli.variants annotate
python -m lhc.cli.variants compare
python -m lhc.cli.variants diff
python -m lhc.cli.variants filter
python -m lhc.cli.variants merge
python -m lhc.cli.variants sample
python -m lhc.cli.variants shift
python -m lhc.cli.variants split_alt
python -m lhc.cli.variants trim_alt
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