fastk 1.0

Python wrappers for FastK tools

FASTK_python

Python interface for FASTK (currently Histex and Profex). Python >= 3 is required.

How to install

$ git clone https://github.com/yoshihikosuzuki/FASTK_python
$ cd FASTK_python
$ make
$ pip3 install .

How to use

Quick usage

import fastk

# Histex
hist = fastk.histex("/path/to/source[.hist]")

# Profex
prof = fastk.profex("/path/to/source[.prof]", read_id=1)

histex()

Signature: fastk.histex(fastk_prefix: str, min_count: int = 1, max_count: int = 100) -> bits.util._counter.RelCounter
Docstring:
Run Histex and return a histogram of k-mer count frequencies.

positional arguments:
  @ fastk_prefix : Prefix of the output files of FastK.

optional arguments:
  @ [min|max]_count : Specify the range of the k-mer count.

profex()

fastk.profex(
    fastk_prefix: str,
    read_id: int,
    zero_padding: bool = False,
    return_k: bool = False,
) -> Union[List[int], Tuple[List[int], int]]
Docstring:
Run Profex and return the k-mer count profile of a single read.

positional arguments:
  @ fastk_prefix : Prefix of the output files of FastK.
  @ read_id      : Read ID (1, 2, ...)
  @ zero_padding : If True, add (K - 1) zero counts to the prefix.
  @ return_k     : If True, return the value of K as well.