o RŀgO@s&dZddZddZGdddZdS)aLarge file parsing of Genepop files. The standard parser loads the whole file into memory. This parser provides an iterator over data. Classes: - LargeRecord - Holds GenePop data. Functions: - read - Parses a GenePop record (file) into a Record object. cs|d\}}|ddd}dd|D}t|ddvr"dnd z fd d|D}WntyAfd d|D}Ynw||fS) z Get individual's data from line.,  cSsg|]}|dkr|qS).0markerrrV/var/www/html/myenv/lib/python3.10/site-packages/Bio/PopGen/GenePop/LargeFileParser.py szget_indiv..)r cs,g|]}t|dt|dfqS)r Nintr marker_lenrr r s csg|] }t|dfqS)r rrrrr r $s)splitreplacelen ValueError)line indiv_name marker_linemarkers allele_listrrr get_indivs   rcCst|}t||_t|dd}|d}|j||}|dkrG|}| dkr9|j dn|j ||}|dks(|}t |\}}|_ |j ||S)zParse a handle containing a GenePop file. Arguments: - handle is a file-like object that contains a GenePop record. rrrPOP)Recordnextrstrip comment_linerr loci_listextendreadlineupperstackappendrr)handlerecordsample_loci_lineall_locir next_linerrrrr read(s$       r-c@s eZdZdZddZddZdS)raHold information from a GenePop record. Members: marker_len The marker length (2 or 3 digit code per allele). comment_line Comment line. loci_list List of loci names. data_generator Iterates over population data. The generator will only work once. If you want to read a handle twice you have to re-open it! data_generator can either be () - an empty tuple - marking a new population or an individual. An individual is something like ('Ind1', [(1,1), (3,None), (200,201)], In the case above the individual is called Ind1, has three diploid loci. For the second loci, one of the alleles is unknown. cCs(||_d|_d|_g|_g|_g|_dS)zInitialize the class.r rN)r(rr!r" populationsr&)selfr(rrr __init__]s  zRecord.__init__c cs|j|jfD]E}|D]@}|}|dkrdVq t|\}}}g}|D]}g}|D]} | dkr8|dq,|| q,|t|q&||fVq qdS)zExtract population data.rrr N)r&r(r r%rr'tuple) r/r(rrrr clean_listlocusmk_realalrrr data_generatorfs$    zRecord.data_generatorN)__name__ __module__ __qualname____doc__r0r6rrrr rEs rN)r:rr-rrrrr s