diff TEisotools-1.1.a/commons/core/coord/Range.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/commons/core/coord/Range.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,363 @@
+# 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))