o Rŀg&@s2dZddlmZddZddZGdddZd S) aFCode to work with GenePop. See http://wbiomed.curtin.edu.au/genepop/ , the format is documented here: http://wbiomed.curtin.edu.au/genepop/help_input.html . Classes: Record Holds GenePop data. Functions: read Parses a GenePop record (file) into a Record object. Partially inspired by MedLine Code. )deepcopycsdd|d\}}|ddd}dd|D}t|dd vr&d nd z fd d|D}WntyGfd d|D}Ynw||fS)z>Extract the details of the individual information on the line.cSst|}|dkr dS|S)z*Return integer of val, or None if is zero.rN)int)valvrO/var/www/html/myenv/lib/python3.10/site-packages/Bio/PopGen/GenePop/__init__.py int_no_zeroszget_indiv..int_no_zero,  cSsg|]}|dkr|qS)r.0markerrrr &szget_indiv..r)rcs,g|]}|d|dfqS)rNrr r marker_lenrrr,scsg|] }|dfqS)rrr rrrr1s)splitreplacelen ValueError)line indiv_name marker_linemarkers allele_listrrr get_indivs   rcCs^t}t||_t|dd}|d}|j||D]}|}|dkr/n |j |q!t d|j g|D]%}|}|dkrU|j gqBt |\}}|_ |j d ||fqB|j}|j D]>}|j |dd|D]/} tt|D]&} | d| } g} | D]} | dkr| d q| | qt| | d| <qq|qn|S) zpParse a handle containing a GenePop file. handle is a file-like object that contains a GenePop record. r r r POPz;No population data found, file probably not GenePop relatedrN)Recordnextrstrip comment_linerr loci_listextendupperappendr populationsrrpop_listrangertuple)handlerecordsample_loci_lineall_locirrrlocipopindivmk_imk_origmk_realalrrrread5sB          r:c@sHeZdZdZddZddZddZdd Zd d Zd d Z ddZ dS)r#aHold 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. - pop_list List of population names. - populations List of population data. In most genepop files, the population name is not trustable. It is strongly recommended that populations are referred by index. populations has one element per population. Each element is itself a list of individuals, each individual is a pair composed by individual name and a list of alleles (2 per marker or 1 for haploids): Example:: [ [ ('Ind1', [(1,2), (3,3), (200,201)], ('Ind2', [(2,None), (3,3), (None,None)], ], [ ('Other1', [(1,1), (4,3), (200,200)], ] ] cCs"d|_d|_g|_g|_g|_dS)zInitialize the class.rr N)rr&r'r,r+)selfrrr__init__s  zRecord.__init__c Cs|jdg}|d|jd|jD]R}|d|D]H}|\}}|||d|D]0}|d|D]&}|dur@d}t|}t||jkrYdd|g}t||jksK||q8q/|dqqd|S)z6Return (reconstruct) a GenePop textual representation. zPop r r N0r )r&r*joinr'r+strrr) r;repr4r5namerrr9aStrrrr__str__s,         zRecord.__str__cCsVi}t|jD]!\}}t}|j|_|j|_t|j|_t|g|_||||<q|S)a$Split a GP record in a dictionary with 1 pop per entry. Given a record with n pops and m loci returns a dictionary of records (key pop_name) where each item is a record with a single pop and m loci. Arguments: - pop_names - Population names ) enumerater+r#rr&rr')r; pop_namesgp_popsi populationgp_poprrr split_in_popss   zRecord.split_in_popsc Csi}t|jD]>\}}t}|j|_|j|_|g|_g|_|jD]}g}|D]}||d|d|gfq&|j|q |||jd<q|S)zSplit a GP record in a dictionary with 1 locus per entry. Given a record with n pops and m loci returns a dictionary of records (key locus name) where each item is a record with a single locus and n pops. rr")rEr'r#rr&r+r*) r;gpgp_locirHlocusrJr4my_popr5rrr split_in_locis zRecord.split_in_locicCs |j|=dS)z"Remove a population (by position).N)r+)r;posrrrremove_populations zRecord.remove_populationcCs0|j|=|jD]}|D] }|\}}||=q qdS)zRemove a locus by position.N)r'r+)r;rQr4r5rBr3rrrremove_locus_by_positions zRecord.remove_locus_by_positioncCs0t|jD]\}}||kr||dSqdS)zRemove a locus by name.N)rEr'rS)r;rBrHrNrrrremove_locus_by_names  zRecord.remove_locus_by_nameN) __name__ __module__ __qualname____doc__r<rDrKrPrRrSrTrrrrr#as" r#N)rXcopyrrr:r#rrrrs  ,