31 projects
edit-sam
Streaming editor for SAM, BAM, and CRAM files.
partake
Shard input to persistent jobs at raw pipe speed.
subfeed
High-throughput I/O coordinator for feeding persistent subprocesses.
dna-methylation
Call DNA methylation on SAM/BAM/CRAM files.
sam-partake
Shard SAM/BAM/CRAM streams to persistent jobs at pipe speed.
amethyst-facet
Compute window aggregations and alter contents of Amethyst HDF5 files
sam-dealer
High-throughput, zero-IO parallel dispatcher for SAM/BAM streams. Distributes reads by index (round-robin) to persistent workers with backpressure management.
bombsquad
Isolate OOM-prone functions in a separate process, raise exceptions on SIGKILL or segfault
scifter-core
Core utils for building single cell processing tools
hich
CLI tools for Hi-C data processing
nonblocking-itertools
None
salish
None
steed
A drop-in replacement for tee with file buffering and output queue management.
partitioned
Determine if a series of lines is partitioned (all identical lines sequential).
smart-open-with-pbgzip
Makes smart_open write to .gz/.gzip files using pbgzip rather than gzip
hich-restrict
None
curry-batch
Curry a list of commands passed as arguments with a YAML list of argument lists, then output the command stdout as a new YAML list of lists.
copyfilter
versus-cli
Run A vs. B analyses, storing analysis input, command and result in YAMLized dataframe. Part of Wistan infrastructure.
dataframe-vis-nb
datavis-cli
Output data loading and visualization boilerplate
pandas-cli
itertools-cli
sanb
nbcell-check-cli
nbformat-cli
notebook-vis-cli
Generate jupyter notebooks preloaded with visualization boilerplate
pathlib-cli
Command line interface for subset of Python's pathlib library to filter for parts of filenames and paths
aclustermap
Convert YAMLized pandas DataFrame to Seaborn clustermap
