s_mart: commons/core/coord/Range.py comparison

comparison commons/core/coord/Range.py @ 38:2c0c0a89fad7

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author	m-zytnicki
date	Thu, 02 May 2013 09:56:47 -0400
parents	769e306b7933
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+# 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 ):
+## 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 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))

Mercurial > repos > yufei-luo > s_mart

comparison commons/core/coord/Range.py @ 38:2c0c0a89fad7