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__init__.py

00001 """This module deals with 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 located at:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8106085&dopt=Abstract

Copyright Jonathan Taylor 2005
"""

00012 class DifferentialCutsite:
    """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.

    """

00026     def __init__(self, **kwds):
        """Initialize a DifferentialCutsite.

        Each member (as listed in the class description) should be included as a
        keyword.
        """
        
        self.start = int(kwds["start"])
        self.enzyme = kwds["enzyme"]
        self.cuts_in = kwds["cuts_in"]
        self.blocked_in = kwds["blocked_in"]

00038 class AlignmentHasDifferentLengthsError(Exception):
    pass

00041 class CAPSMap:
    """A 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.
    """

00050     def __init__(self, alignment, enzymes = []):
        """Initialize the CAPSMap

        Required:
        alignment    The alignment to be mapped.

        Optional:
        enzymes      The enzymes to be used to create the map.
        """

        self.sequences = [rec.seq for rec in alignment.get_all_seqs()]
        self.size = len(self.sequences)
        self.length = len(self.sequences[0])
        for seq in self.sequences:
            if len(seq) != self.length:
                raise AlignmentHasDifferentLengthsError

        self.alignment = alignment
        self.enzymes = enzymes

        # look for dcuts
        self._digest()
    
    def _digest_with(self, enzyme):
        cuts = {}
        all = []

        # go through each sequence
        for seq in self.sequences:

            # grab all the cuts in the sequence
            cuts[seq] = [cut - enzyme.fst5 for cut in enzyme.search(seq)]

            # maintain a list of all cuts in all sequences
            all.extend(cuts[seq])

        # we sort the all list and remove duplicates
        all.sort()
        
        last = -999
        new = []
        for cut in all:
            if cut != last:
                new.append(cut)
            last = cut

        all = new
        # all now has indices for all sequences in the alignment

        for cut in all:
            # test for dcuts

            cuts_in = []
            blocked_in = []

            for i in range(0, self.size):
                seq = self.sequences[i]
                if cut in cuts[seq]:
                    cuts_in.append(i)
                else:
                    blocked_in.append(i)

            if cuts_in != [] and blocked_in != []:
                self.dcuts.append(DifferentialCutsite(start = cut, enzyme = enzyme, cuts_in = cuts_in, blocked_in = blocked_in))

    def _digest(self):
        self.dcuts = []

        for enzyme in self.enzymes:
            self._digest_with(enzyme)

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