scripts

gwas_tools.automation.scripts.generate_algo_script(name, env, plots=False, imfs=None, imf_thr=-1.0, omg_thr=-1.0, harmonics=None, fig_ext='png', fig_size=None)

Generate the script for the main algorithm.

Parameters:

• name (str) – name of the script

• env (str) – python3 environment shebang

• plots (bool, optional) – generate (or not) plots during the analysis (default : False)

• imfs (list[int], optional) – imfs to plot (default : None, i.e. all the imfs)

• imf_thr (float, optional) – correlation value above which to plot imfs (default : -1.0)

• omg_thr (float, optional) – correlation value above which to plot omegagrams (default : -1.0)

• harmonics (list[int]) – harmonics for the culprit (default : [1, 3, 5])

• fig_ext (str, optional) – plots extension (default : png)

• fig_size (tuple[int], optional) – figure size

gwas_tools.automation.scripts.generate_algo_corr_script(name, env, plots=False, imfs=None, imf_thr=-1.0, fig_ext='png', fig_size=None)

Generate the script for the main correlation algorithm.

Parameters:

• name (str) – name of the script

• env (str) – python3 environment shebang

• plots (bool, optional) – generate (or not) plots during the analysis (default : False)

• imfs (list[int], optional) – imfs to plot (default : None, i.e. all the imfs)

• imf_thr (float, optional) – correlation value above which to plot imfs (default : -1.0)

• fig_ext (str, optional) – plots extension (default : png)

• fig_size (tuple[int], optional) – figure size

gwas_tools.automation.scripts.generate_comparison_script(name, env, html=False, imfs=None, summary_imfs=1, imf_thr=-1.0, fig_ext='png', fig_size=None, html_abs_path='')

Generate the script for the analysis’ results comparison.

Parameters:

• name (str) – name of the script

• env (str) – python3 environment shebang

• html (bool, optional) – if True, the summary web page is generated (default : False)

• imfs (list[int], optional) – imfs to print in the summary table (default : None)

• summary_imfs (int, optional) – imfs to show in the summary web page for each day (default : 1)

• imf_thr (float, optional) – correlation value above which to consider a line in the summary table (default : -1.0)

• fig_ext (str, optional) – plots extension (default : png)

• fig_size (tuple[int], optional) – figure size

• html_abs_path (str, optional) – absolute path for files and images in the html page (default : “”)

gwas_tools.automation.scripts.generate_comparison_corr_script(name, env, html=False, imfs=None, html_abs_path='')

Generate the script for the correlation analysis’ results comparison.

Parameters:

• name (str) – name of the script

• env (str) – python3 environment shebang

• html (bool, optional) – if True, the summary web page is generated (default : False)

• imfs (list[int], optional) – imfs to print in the summary table (default : None)

• html_abs_path (str, optional) – absolute path for files and images in the html page (default : “”)

gwas_tools.automation.scripts.generate_condor_post_script(name)

Generate the condor post script to allow main jobs failure.

Parameters:

name (str) – name of the condor post script