Quickstart

Initialize DB

import pymisha as pm

pm.gdb_init("/path/to/misha_db")

Extract values

intervals = pm.gintervals_from_strings(["chr1:0-1000", "chr1:2000-2600"])
out = pm.gextract("track1", intervals, iterator=100)

Screen and summarize

filtered = pm.gscreen("track1 > 0.5", intervals)
stats = pm.gsummary("track1", intervals)

Thread safety

PyMisha is not thread-safe. All state (active database, virtual tracks, config) is process-global, so you should not call PyMisha from multiple threads or open more than one database per process. See the README for full details.

Example DB

pm.gdb_init_examples()
print(pm.gtrack_ls())
print(pm.gextract("dense_track", pm.gintervals("chr1", 0, 1000)))