lhc-python 2.5.1

My personal package for bioinformatics related stuff

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