pyft 0.1.5

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pyft: python bindings for fibertools-rs

pyft provides a python API for the rust library fibertools-rs. The inspiration for this API is to make analysis in python easier and faster; therefore, only extraction of data from a fiberseq bam is supported and not writing.

Install

pip install pyft

Example

import pyft
# bam file with ~3X coverage of chr20
bam_f = "../tmp.bam"
fiberdata = pyft.FiberdataFetch(bam_f, "chr20", 0, 10_000_000)
for idx, fiber in enumerate(fiberdata):
    if idx < 10:
        # print some info about the fiber
        print(fiber)
    # the number of ccs passes
    fiber.ec
    # the mps start positions
    fiber.msp.starts
    # print the nuc reference starts
    fiber.nuc.reference_starts
    # lift query (fiber) positions to reference positions
    fiber.lift_query_positions([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
    # lift reference positions to query (fiber) positions
    fiber.lift_reference_positions([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
    # aligned blocks between query (fiber) and reference 
    fiber.get_aligned_blocks_as_ranges()

Documentation

The documentation for pyft can be found on readthedocs.