Ri^dZddlmZddlmZGddZGddeZGdd Zy ) 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 )MultipleSeqAlignment)SeqceZdZdZdZy)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. c ft|d|_|d|_|d|_|d|_y)zInitialize a DifferentialCutsite. Each member (as listed in the class description) should be included as a keyword. startenzymecuts_in blocked_inN)intrr r r )selfkwdss I/home/agent/.friday_env/lib/python3.12/site-packages/Bio/CAPS/__init__.py__init__zDifferentialCutsite.__init__$s6 g' 8n I |,N)__name__ __module__ __qualname____doc__rrrrrs   -rrceZdZdZy)!AlignmentHasDifferentLengthsErrorz>Exception where sequences in alignment have different lengths.N)rrrrrrrrr0sHrrc$eZdZdZddZdZdZy)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. Nc|g}t|tr|Dcgc]}|jc}|_t |j|_t |jd|_|jD] }t ||j k7stn7|Dcgc] }t|c}|_|j\|_|_||_ ||_ |jycc}wcc}w)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. Nr) isinstancerseq sequenceslensizelengthrrshape alignmentenzymes_digest)r r#r$recrss rrzCAPSMap.__init__>s ?G i!5 61:;#cgg;DNDNN+DIdnnQ/0DK~~ <s8t{{*;; </88c!f8DN%.__ "DIt{"  <9s C1C6c g}g}|jD]O}|j|Dcgc]}||jz }}|j||j |Qt t |}|D]{}g}g}t|jD]/\} }||| vr|j | |j | 1|sQ|sT|jj t||||}ycc}w)N)rr r r ) rsearchfst5extendappendsortedset enumeratedcutsr) r r cuts all_seq_cutsrcutseq_cutsr r is r _digest_withzCAPSMap._digest_with\s >> "C5;]]35GHcfkk)HHH    ) KK !  "c,/0  CGJ#DNN3 )3$q'>NN1%%%a(  ) : !!'!&'j IsC8cVg|_|jD]}|j|yN)r0r$r6)r r s rr%zCAPSMap._digest~s* ll &F   f % &rr8)rrrrrr6r%rrrrr4s< D&rrN) r Bio.AlignrBio.Seqrr Exceptionrrrrrr<s6 +--8I IN&N&r