IPTK.IO package¶
Submodules¶
IPTK.IO.InFunctions module¶
IPTK.IO.MEMEInterface module¶
The module contains functions to to call meme software via a system call.
- IPTK.IO.MEMEInterface.call_meme(input_fasta_file: str, output_dir: str, verbose: bool = True, objfunc: str = 'classic', test: str = 'mhg', use_llr: bool = False, shuf: int = 2, hsfrac: float = 0.5, cefrac: float = 0.25, searchsize: int = - 1, maxsize: int = - 1, norand: bool = False, csites: int = - 1, seed: int = - 1, mod: str = 'oops', nmotifs: int = - 1, evt: float = - 1.0, time: int = - 1, nsite: int = - 1, minsites: int = - 1, maxsite: int = - 1, nsites: int = - 1, w: int = - 1, minw: int = - 1, maxw: int = - 1, nomatrim: bool = False, wg: int = - 1, ws: int = - 1, noendgaps: bool = False, maxiter: int = - 1, prior: str = 'dirichlet', b: int = - 1, p: int = - 1) None¶
warper for making a system call to meme software for sequence motif finding for the reset of the function parameters use the function get_meme_help defined in the module IO, submodule MEMEInterface.
- Parameters
input_fasta_file (str) – The path to input FASTA files.
output_dir (str) – the output dir to write the results, IT WILL OVERWRITE EXISTING DIRECTORY
verbose (bool) – whether or not to print the output of calling meme to the screen, default is True.
- IPTK.IO.MEMEInterface.get_meme_help() None¶
Print the command line help interface for the meme tool
- Raises
FileNotFoundError – if meme is not callable
- IPTK.IO.MEMEInterface.is_meme_callable() bool¶
- Returns
True if meme is callable, False otherwise.
- Return type
bool