a h*@szddlZddlZddlmZddlmZddlmZddlm Z m Z m Z m Z ddl ZddlZddlZddlZddlZddlmZddlmZGdd d eZGd d d eZd*e ee ee eeed ddZeedddZ d+e eefeddddZ!d,e eefeddddZ"ee#edddZ$ddZ%ddZ&d-e ee eed d!d"Z'd#d$Z(d%d&Z)ed'd(d)Z*dS).N)partial)islice)Path)IterableIteratorOptionalUnion)logger) betabinomc@seZdZdZdS)ConfigzBConfig contains the parameters related to specific alignment file.N)__name__ __module__ __qualname____doc__rrZ/mounts/lovelace/software/anaconda3/envs/py39/lib/python3.9/site-packages/metaDMG/utils.pyr sr c@s\eZdZdZeedddZeedddZeddd Z edd d Z d dd dZ d S)ConfigszkConfigs contains the parameters related to config file. Inherits from dict. Implements iterations. )returnccs|dd}|dd}|d}|D]}t|}||d<|d||d<||d|d<|d dkr~||d |d <n||d |d <||d |d<||d|d<|dd||d<||d|d<|Vq(dS)zjIteration Yields ------ Iterator[Config] Allow for iteration output_dirlcaZpmdsamplessamplebamz.mismatches.txt.gzZpath_mismatches_txt damage_modez.mismatches.stat.txt.gzZpath_mismatches_statz .stat.txtz .lca.txt.gzZpath_lcaz.log.txtZ path_lca_logtmppath_tmpz .pmd.txt.gzpath_pmdN)keysr )selfZdir_lcaZdir_pmdrrconfigrrr__iter__ s"     zConfigs.__iter__)nrcCstt||dS)zGets the n'th config Parameters ---------- n The index Returns ------- Config A single configuration N)nextr)rr!rrrget_nthAs zConfigs.get_nthcCs |jddS)zpGet the first config Returns ------- Config A single configuration r)r!)r#rrrr get_firstPszConfigs.get_firstcCst|dS)zmThe number of configs Returns ------- int The number of configs r)lenrr$rrr__len__ZszConfigs.__len__NcCst|dt|d}|d}||}tjdd}tjdd}||kr`td|d|d n ||krtd|d |d d S) zECompare the number of configs to the number of parallel_samples used.parallel_samplesrcores_per_sampleT)ZlogicalFzThe total number of jobs z0 are higher than the number of parallel_samples z. 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