Mercurial > repos > urgi-team > teiso
diff TEisotools-1.1.a/commons/core/coord/Range.py @ 16:836ce3d9d47a draft default tip
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| author | urgi-team |
|---|---|
| date | Thu, 21 Jul 2016 07:42:47 -0400 |
| parents | 255c852351c5 |
| children |
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--- a/TEisotools-1.1.a/commons/core/coord/Range.py Thu Jul 21 07:36:44 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,363 +0,0 @@ -# Copyright INRA (Institut National de la Recherche Agronomique) -# http://www.inra.fr -# http://urgi.versailles.inra.fr -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. - - -## Record a region on a given sequence -# -class Range( object ): - - __slots__ = ("seqname", "start", "end", '__dict__') - - ## Constructor - # - # @param seqname the name of the sequence - # @param start the start coordinate - # @param end the end coordinate - # - def __init__(self, seqname="", start=-1, end=-1): - self.seqname = seqname - self.start = int(start) - self.end = int(end) - - ## Equal operator - # - # @param o a Range instance - # - def __eq__(self, o): - if type(o) is type(self) and self.seqname == o.seqname and self.start == o.start and self.end == o.end: - return True - return False - - ## Unequal operator - # - # @param o a Range instance - # - def __ne__(self, o): - return not self.__eq__(o) - - ## Convert the object into a string - # - # @note used in 'print myObject' - # - def __str__( self ): - return self.toString() - - ## Convert the object into a string - # - # @note used in 'repr(myObject)' for debugging - # - def __repr__( self ): - return self.toString().replace("\t",";") - - def setStart(self, start): - self.start = start - - def setEnd(self, end): - self.end = end - - def setSeqName(self, seqName): - self.seqname = seqName - - ## Reset - # - def reset(self): - self.seqname = "" - self.start = -1 - self.end = -1 - - ## Return the attributes as a formatted string - # - def toString(self): - string = "%s" % (self.seqname) - string += "\t%d" % (self.start) - string += "\t%d" % (self.end) - return string - - ## Show the attributes - # - def show(self): - print self.toString() - - ## Return seqname - # - def getSeqname(self): - return self.seqname - - ## Return the start coordinate - # - def getStart(self): - return self.start - - ## Return the end coordinate - # - def getEnd(self): - return self.end - - ## Return the lowest value between start and end coordinates - # - def getMin(self): - return min(self.start, self.end) - - ## Return the greatest value between start and end attributes - # - def getMax(self): - return max(self.start, self.end) - - ## Return True if the instance is on the direct strand, False otherwise - # - def isOnDirectStrand(self): - if self.start <= self.end: - return True - else: - return False - - ## Return True if the instance is on the reverse strand, False otherwise - # - def isOnReverseStrand(self): - return not self.isOnDirectStrand() - - ## Return '+' if the instance is on the direct strand, '-' otherwise - # - def getStrand(self): - if self.isOnDirectStrand(): - return '+' - else: - return '-' - - ## Exchange start and end coordinates - # - def reverse(self): - tmp = self.start - self.start = self.end - self.end = tmp - - ## Return the length of the instance - # - # @warning old name is 'length' - # - def getLength(self): - return int(abs(self.start-self.end))+1 - - ## Return True if the instance is empty, False otherwise - # - def isEmpty(self): - if self.start==self.end and (self.start==0 or self.start==-1): - return True - return False - - ## Set attributes from tuple - # - # @param tuple a tuple with (name,start,end) - # - def setFromTuple(self, tuple): - self.seqname = tuple[0] - self.start = int(tuple[1]) - self.end = int(tuple[2]) - - ## Set attributes from string - # - # @param string a string formatted like name<sep>start<sep>end - # @param sep field separator - # - def setFromString(self, string, sep="\t"): - if string[-1] == "\n": - string = string[:-1] - self.setFromTuple( string.split(sep) ) - - ## Merge the instance with another Range instance - # - # @param o a Range instance - # - def merge(self, o): - if self.seqname != o.seqname: - return - if self.isOnDirectStrand(): - self.start = min(self.getMin(), o.getMin()) - self.end = max(self.getMax(), o.getMax()) - else: - self.start = max(self.getMax(), o.getMax()) - self.end = min(self.getMin(), o.getMin()) - - ## Return True if the instance overlaps with another Range instance, False otherwise - # - # @param o a Range instance - # - def isOverlapping(self, o): - if o.seqname != self.seqname: - return False - smin = self.getMin() - smax = self.getMax() - omin = o.getMin() - omax = o.getMax() - if omin <= smin and omax >= smax: - return True - if omin >= smin and omin <= smax or omax >= smin and omax <= smax: - return True - return False - - - ## Return the length of the overlap between the instance and another Range, 0 if no overlap - # - # @param o a Range instance - # - def getOverlapLength( self, o ): - if self.isOverlapping( o ): - if self.isIncludedIn( o ): - return self.getLength() - elif o.isIncludedIn( self ): - return o.getLength() - elif o.getMin() <= self.getMax() and o.getMin() >= self.getMin(): - return self.getMax() - o.getMin() + 1 - elif o.getMax() <= self.getMax() and o.getMax() >= self.getMin(): - return o.getMax() - self.getMin() + 1 - return 0 - - - ## Return True if the instance is included within another Range, False otherwise - # - # @param o a Range instance - # - # @note the min (respectively max) coordinates can be equal - # - def isIncludedIn( self, o ): - if o.seqname != self.seqname: - return False - if self.getMin() >= o.getMin() and self.getMax() <= o.getMax(): - return True - else: - return False - - - ## Return the distance between the start of the instance and the start of another Range instance - # - # @param o a Range instance - # - def getDistance(self, o): - if self.isOnDirectStrand() == o.isOnDirectStrand(): - if self.isOverlapping(o): - return 0 - elif self.isOnDirectStrand(): - if self.start > o.start: - return self.start - o.end - else: - return o.start - self.end - else: - if self.start > o.start: - return self.end - o.start - else: - return o.end - self.start - return -1 - - ## Remove in the instance the region overlapping with another Range instance - # - # @param o a Range instance - # - def diff(self, o): - new_range = Range(self.seqname) - if not self.isOverlapping(o) or self.seqname != o.seqname: - return new_range - - istart = min(self.start, self.end) - iend = max(self.start, self.end) - jstart = min(o.start, o.end) - jend = max(o.start, o.end) - if istart < jstart: - if iend <= jend: - if self.isOnDirectStrand(): - self.start = istart - self.end = jstart - 1 - else: - self.start = jstart - 1 - self.end = istart - else: - if self.isOnDirectStrand(): - self.start = istart - self.end = jstart - 1 - new_range.start = jend + 1 - new_range.end = iend - else: - self.start = jstart - 1; - self.end = istart; - new_range.start = iend - new_range.end = jend + 1 - else: #istart>=jstart - if iend <= jend: - self.start = 0 - self.end = 0 - else: - if self.isOnDirectStrand(): - self.start = jend + 1 - self.end = iend - else: - self.start = iend - self.end = jend + 1 - return new_range - - ## Find the bin that contains the instance and compute its index - # - # @note Required for coordinate indexing via a hierarchical bin system - # - def findIdx(self): - min_lvl = 3 - max_lvl = 6 - for bin_lvl in xrange(min_lvl, max_lvl): - if getBin(self.start, bin_lvl) == getBin(self.end, bin_lvl): - return getIdx(self.start, bin_lvl) - return getIdx(self.start, max_lvl) - - ## Get a bin for fast database access - # - # @return bin number (float) - # - def getBin(self): - for i in xrange(3, 8): - bin_lvl = pow(10, i) - if int(self.start/bin_lvl) == int(self.end/bin_lvl): - return float(bin_lvl+(int(self.start/bin_lvl)/1e10)) - bin_lvl = pow(10, 8) - return float(bin_lvl+(int(self.start/bin_lvl)/1e10)) - - -# Functions - -# Get the bin number of a coordinate according to the bin level. Required for coordinate indexing with hierarchical bin system -# -def getBin(val, bin_lvl): - bin_size = pow(10, bin_lvl) - return long(val / bin_size) - -# Get an index from a coordinate according to the bin level. Required for coordinate indexing with hierarchical bin system -# -def getIdx(val, bin_lvl): - min_lvl = 3 - max_lvl = 6 - if bin_lvl >= max_lvl: - return long((bin_lvl-min_lvl+1)*pow(10,max_lvl)) - return long(((bin_lvl-min_lvl+1)*pow(10,max_lvl))+getBin(val,bin_lvl))