31 projects
dark-matter
Python library and utility scripts for working with genetic sequence data.
extract-soft-clipped
Extract soft-clipped sequences from BAM/SAM files
beast2-xml
Command line script and Python class for generating BEAST2 XML config files.
midsplit
Demultiplex multi-reference BAM files into per-reference buckets and call consensus
tidycols
Align columns of data read from standard input
midtools
Command line scripts and Python classes for detecting multiple infections from NGS reads.
xgrep
xgrep: A grep for Excel (and CSV/TSV) files.
gb2seq
Python library and scripts for working with unannotated sequences based on an annotated reference genome provided by a GenBank file.
rpnpy
Control an RPN calculator from Python.
prseq
Python tools (backed by Rust) for sequence analysis
vsplit
Virtually split a file based on a pattern.
summarize-ranges
Summarize contiguous ranges of integers found on standard input.
viral-rna-simulation
A simulation of replication of viral RNA
seqgen
Command line script and Python class for generating genetic sequence data in FASTA format.
ggrep
Grid grep - search rectangular 'gridded' files, such as Excel, TSV, and CSV.
slurm-pipeline
A Python class and utility script for scheduling SLURM jobs.
pegwords
Python library and scripts for converting digits to mnemonic pegwords and back.
sars2seq
Python library and scripts for working with SARS-CoV-2 sequences.
pystdin
Wrap command-line Python code in a loop over standard input.
daudin
A UNIX command-line shell based on Python
py3seq
Python class providing an interface to the 3seq recombination detection program.
phylo-color
Color the nodes of a phylogenetic tree using regular expressions to match taxa names.
sausage-machine
A Python class for running / scheduling pipeline jobs
gor4
Python class providing an interface to GOR4 amino acid structure prediction C code.
txretry
A Twisted class for retrying failing calls with a customizable back-off schedule.
txRDQ
A Twisted class for queueing and dispatching jobs in a controlled manner.
txdlo
A Twisted class for observing a set of deferreds.
shared_clipboard
Classes for saving, retrieving and clearing shared clipboards stored in Fluidinfo.
txdpce
A Twisted class for parallel execution of functions performing the same task, returning the result from the one that finishes first.
compset
A Python set class that allows complements.
