o Rŀg@sLdZddlmZddlmZGdddZGdddeZGdd d Zd S) alCleaved amplified polymorphic sequence (CAPS) markers. A CAPS marker is a location a DifferentialCutsite as described below and a set of primers that can be used to visualize this. More information can be found in the paper `Konieczny and Ausubel (1993)`_ (PMID 8106085). .. _`Konieczny and Ausubel (1993)`: https://doi.org/10.1046/j.1365-313X.1993.04020403.x )MultipleSeqAlignmentSeqc@seZdZdZddZdS)DifferentialCutsiteaDifferential enzyme cutsite in an alignment. A differential cutsite is a location in an alignment where an enzyme cuts at least one sequence and also cannot cut at least one other sequence. Members: - start - Where it lives in the alignment. - enzyme - The enzyme that causes this. - cuts_in - A list of sequences (as indexes into the alignment) the enzyme cuts in. - blocked_in - A list of sequences (as indexes into the alignment) the enzyme is blocked in. cKs0t|d|_|d|_|d|_|d|_dS)zInitialize a DifferentialCutsite. Each member (as listed in the class description) should be included as a keyword. startenzymecuts_in blocked_inN)intrrrr )selfkwdsr E/var/www/html/myenv/lib/python3.10/site-packages/Bio/CAPS/__init__.py__init__$s  zDifferentialCutsite.__init__N)__name__ __module__ __qualname____doc__rr r r rrs rc@seZdZdZdS)!AlignmentHasDifferentLengthsErrorz>Exception where sequences in alignment have different lengths.N)rrrrr r r rr0src@s*eZdZdZd ddZddZddZdS) CAPSMapzA map of an alignment showing all possible dcuts. Members: - alignment - The alignment that is mapped. - dcuts - A list of possible CAPS markers in the form of DifferentialCutsites. NcCs|durg}t|tr1dd|D|_t|j|_t|jd|_|jD] }t||jkr/tq$ndd|D|_|j\|_|_||_||_ | dS)zInitialize the CAPSMap. Required: - alignment - The alignment to be mapped. Optional: - enzymes - List of enzymes to be used to create the map. Defaults to an empty list. NcSsg|]}|jqSr )seq).0recr r r Lsz$CAPSMap.__init__..rcSsg|]}t|qSr r)rsr r rrSs) isinstancer sequenceslensizelengthrshape alignmentenzymes_digest)r r!r"rr r rr>s      zCAPSMap.__init__c sg}g}|jD]}fdd|D}||||qtt|}|D]1}g}g}t|jD]\} }||| vrC|| q3|| q3|rY|rY|jt|||dq(dS)Ncsg|]}|jqSr )fst5)rcutrr rrcsz(CAPSMap._digest_with..)rrrr ) rsearchextendappendsortedset enumeratedcutsr) r rcuts all_seq_cutsrseq_cutsr%rr ir r&r _digest_with\s,       zCAPSMap._digest_withcCs g|_|jD]}||qdSN)r-r"r2)r rr r rr#~s  zCAPSMap._digestr3)rrrrrr2r#r r r rr4s   "rN) r Bio.AlignrBio.Seqrr Exceptionrrr r r rs