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.
