diff TEisotools-1.1.a/commons/core/seq/BioseqDB.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/commons/core/seq/BioseqDB.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,494 @@
+# 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.
+
+
+import sys
+import re
+from commons.core.seq.Bioseq import Bioseq
+from commons.core.stat.Stat import Stat
+
+
+## Handle a collection of a Bioseq (header-sequence) 
+#
+class BioseqDB( object ):
+    
+    def __init__( self, name="" ):
+        self.idx = {}
+        self.idx_renamed = {}
+        self.db = []
+        self.name = name
+        if name != "":
+            faFile = open( name )
+            self.read( faFile )
+            faFile.close()
+        self.mean_seq_lgth = None
+        self.stat = Stat()
+        
+        
+    ## Equal operator
+    #
+    def __eq__( self, o ):
+        if type(o) is type(self):
+            selfSize = self.getSize()
+            if selfSize != o.getSize():
+                return False
+            nbEqualInstances = 0
+            for i in self.db:
+                atLeastOneIsEqual = False
+                for j in o.db:
+                    if i == j:
+                        atLeastOneIsEqual = True
+                        continue
+                if atLeastOneIsEqual:
+                    nbEqualInstances += 1
+            if nbEqualInstances == selfSize:
+                return True
+        return False
+    
+    ## Not equal operator
+    #
+    def __ne__(self, o):
+        return not self.__eq__(o)
+    
+    ## Change the name of the BioseqDB
+    #
+    # @param name the BioseqDB name
+    # 
+    def setName(self, name):
+        self.name = name
+        
+        
+    ## Record each sequence of the input file as a list of Bioseq instances
+    #
+    # @param faFileHandler handler of a fasta file
+    #
+    def read( self, faFileHandler ):
+        while True:
+            seq = Bioseq()
+            seq.read( faFileHandler )
+            if seq.sequence == None:
+                break
+            self.add( seq )
+            
+            
+    ## Write all Bioseq of BioseqDB in a formatted fasta file (60 character long)
+    #
+    # @param faFileHandler file handler of a fasta file
+    #
+    def write( self, faFileHandler ):
+        for bs in self.db:
+            bs.writeABioseqInAFastaFile( faFileHandler )
+            
+            
+    ## Write all Bioseq of BioseqDB in a formatted fasta file (60 character long)
+    #
+    # @param outFaFileName file name of fasta file
+    # @param mode 'write' or 'append'
+    #
+    def save( self, outFaFileName, mode="w" ):
+        outFaFile = open( outFaFileName, mode )
+        self.write( outFaFile )
+        outFaFile.close()
+        
+        
+    ## Read a formatted fasta file and load it in the BioseqDB instance
+    #
+    # @param inFaFileName file name of fasta file
+    #    
+    def load(self, inFaFileName):
+        fichier = open(inFaFileName)
+        self.read(fichier)
+        fichier.close()
+        
+        
+    ## Reverse each sequence of the collection
+    #
+    def reverse( self ):
+        for bs in self.db:
+            bs.reverse()
+            
+            
+    ## Turn each sequence into its complement
+    #
+    def complement( self ):
+        for bs in self.db:
+            bs.complement()
+            
+            
+    ## Reverse and complement each sequence
+    #
+    def reverseComplement( self ):
+        for bs in self.db:
+            bs.reverseComplement()
+            
+            
+    ## Set the collection from a list of Bioseq instances
+    #
+    def setData( self, lBioseqs ):
+        for i in lBioseqs:
+            self.add( i )
+            
+            
+    ## Initialization of each attribute of the collection
+    #
+    def reset( self ):
+        self.db = []
+        self.idx = {}
+        self.name = None
+        self.mean_seq_lgth = None
+        self.stat.reset()
+        
+        
+    ## Remove all the gap of the sequences of the collection
+    #
+    def cleanGap(self): 
+        for iBioSeq in self.db:
+            iBioSeq.cleanGap()
+            
+            
+    ## Add a Bioseq instance and update the attributes
+    #
+    # @param bs a Bioseq instance
+    # 
+    def add( self, bs ):
+        if self.idx.has_key( bs.header ):
+            sys.stderr.write( "ERROR: two sequences with same header '%s'\n" % ( bs.header ) )
+            sys.exit(1)
+        self.db.append( bs )
+        self.idx[ bs.header ] = len(self.db) - 1
+        self.idx_renamed[ bs.header.replace("::","-").replace(":","-").replace(",","-").replace(" ","_") ] = len(self.db) - 1
+        
+        
+    ## Give the Bioseq instance corresponding to specified index
+    #
+    # @return a Bioseq instance
+    #
+    def __getitem__(self,index):
+        if index < len(self.db):
+            return self.db[index]
+        
+        
+    ## Give the number of sequences in the bank
+    #
+    # @return an integer
+    #
+    def getSize( self ):
+        return len( self.db )
+    
+    
+    ## Give the cumulative sequence length in the bank
+    #
+    # @return an integer
+    #
+    def getLength( self ):
+        cumLength = 0
+        for iBioseq in self.db:
+            cumLength += iBioseq.getLength()
+
+        return cumLength
+    
+    
+    ## Return the length of a given sequence via its header
+    #
+    # @return an integer
+    #
+    def getSeqLength( self, header ):
+        return self.fetch(header).getLength()
+    
+    
+    ## Return a list with the sequence headers
+    #
+    def getHeaderList( self ):
+        lHeaders = []
+        for bs in self.db:
+            lHeaders.append( bs.header )
+        return lHeaders
+    
+    
+    ## Return a list with the sequences
+    #
+    def getSequencesList( self ):
+        lSeqs = []
+        for bs in self.db:
+            lSeqs.append( bs.getSequence() )
+        return lSeqs
+    
+    
+    ## Give the Bioseq instance of the BioseqDB specified by its header
+    # 
+    # @warning name of this method not appropriate getBioseqByHeader is proposed
+    # @param header string
+    # @return a Bioseq instance
+    #
+    def fetch( self, header ):
+        idx = self.idx.get(header,None)
+        if idx is not None:
+            return self.db[idx]
+        else:
+            idx = self.idx_renamed.get(header,None)
+            if idx is not None:
+                return self.db[idx]
+            else:
+                raise Exception("Header: "+header+" not found")
+    
+    
+    ## Get a list of Bioseq instances based on a list of headers
+    #
+    # @param lHeader list
+    # @return a list of Bioseq instances
+    #
+    def fetchList( self, lheader ):
+        result = []
+        for headerName in lheader: 
+            result.append(self.fetch( headerName ))
+        return result
+    
+    
+    ## Sort self on its Bioseq size, possibly by decreasing length
+    # 
+    # @param reverse boolean
+    #
+    def sortByLength(self, reverse = False):
+        self.db.sort(key = lambda iBS: iBS.getLength(), reverse = reverse)
+    
+
+    ## Give the Bioseq instance of the BioseqDB specified by its renamed header
+    # In renamed header "::", ":", "," character are been replaced by "-" and " " by "_"
+    #
+    # @param renamedHeader string
+    # @return a Bioseq instance
+    #
+    def getBioseqByRenamedHeader( self, renamedHeader ):
+        return self.db[self.idx_renamed[renamedHeader]]
+    
+    
+    ## Count the number of times the given nucleotide is present in the bank.
+    #
+    # @param nt character (nt or aa)
+    # @return an integer
+    #
+    def countNt( self, nt ):
+        total = 0
+        for iBioseq in self.db:
+            total+= iBioseq.countNt( nt )
+        return total
+    
+    
+    ## Count the number of times each nucleotide (A,T,G,C,N) is present in the bank.
+    #
+    # @return a dictionary with nucleotide as key and an integer as values
+    #
+    def countAllNt( self ):
+        dNt2Count = {}
+        for nt in ["A","T","G","C","N"]:
+            dNt2Count[ nt ] = self.countNt( nt )
+        return dNt2Count
+    
+    
+    ## Extract a sub BioseqDB of specified size which beginning at specified start
+    #
+    # @param start integer index of first included Bioseq
+    # @param size integer size of expected BioseqDB 
+    # @return a BioseqDB
+    #
+    def extractPart(self, start, size):
+        iShorterBioseqDB = BioseqDB()
+        for iBioseq in self.db[start:(start + size)]:
+            iShorterBioseqDB.add(iBioseq)    
+        return iShorterBioseqDB  
+    
+    
+    ## Extract a sub BioseqDB with the specified number of best length Bioseq
+    #
+    # @param numBioseq integer the number of Bioseq searched
+    # @return a BioseqDB
+    #
+    def bestLength(self, numBioseq):
+        length_list = []
+        numseq = 0
+        for each_seq in self.db:
+            if each_seq.sequence == None:
+                l=0
+            else:
+                l = each_seq.getLength()
+            length_list.append(l)
+            numseq = numseq + 1
+
+        length_list.sort()
+        size = len(length_list)
+        if numBioseq < size:
+            len_min = length_list[size-numBioseq]
+        else:
+            len_min = length_list[0]
+
+        numseq = 0
+        nbsave = 0
+        bestSeqs = BioseqDB()
+        bestSeqs.setName(self.name)
+        for each_seq in self.db:
+            if each_seq.sequence == None:
+                l=0 
+            else :
+                l = each_seq.getLength()
+            numseq = numseq + 1
+            if l >= len_min:
+                bestSeqs.add(each_seq)
+                nbsave = nbsave + 1
+            if nbsave == numBioseq :
+                break      
+        return bestSeqs
+    
+    
+    ## Extract a sub BioseqDB from a file with Bioseq header containing the specified pattern
+    #
+    # @param pattern regular expression of wished Bioseq header
+    # @param inFileName name of fasta file in which we want extract the BioseqDB
+    #
+    def extractPatternOfFile(self, pattern, inFileName):
+        if pattern=="" :
+            return
+        srch=re.compile(pattern)
+        file_db=open(inFileName)
+        numseq=0
+        nbsave=0
+        while 1:
+            seq=Bioseq()
+            seq.read(file_db)
+            if seq.sequence==None:
+                break
+            numseq+=1
+            m=srch.search(seq.header)
+            if m:
+                self.add(seq)
+                nbsave+=1
+        file_db.close()
+        
+        
+    ## Extract a sub BioseqDB from the instance with all Bioseq header containing the specified pattern
+    #
+    # @param pattern regular expression of wished Bioseq header
+    #
+    # @return a BioseqDB
+    #
+    def getByPattern(self,pattern):
+        if pattern=="" :
+            return
+        iBioseqDB=BioseqDB()
+        srch=re.compile(pattern)
+        for iBioseq in self.db:
+            if srch.search(iBioseq.header):
+                iBioseqDB.add(iBioseq)
+        return iBioseqDB
+    
+    
+    ## Extract a sub BioseqDB from the instance with all Bioseq header not containing the specified pattern
+    #
+    # @param pattern regular expression of not wished Bioseq header
+    #
+    # @return a BioseqDB
+    #
+    def getDiffFromPattern(self,pattern):
+        if pattern=="" :
+            return
+        iBioseqDB=BioseqDB()
+        srch=re.compile(pattern)
+        for iBioseq in self.db:
+            if not srch.search(iBioseq.header):
+                iBioseqDB.add(iBioseq)
+        return iBioseqDB
+    
+    #TODO: to run several times to remove all concerned sequences when big data. How to fix it ?
+    ## Remove from the instance all Bioseq which header contains the specified pattern
+    #
+    # @param pattern regular expression of not wished Bioseq header
+    #
+    def rmByPattern(self,pattern):
+        if pattern=="" :
+            return
+        srch=re.compile(pattern)
+        for seq in self.db:
+            if srch.search(seq.header):
+                self.db.remove(seq)     
+                
+                
+    ## Copy a part from another BioseqDB in the BioseqDB if Bioseq have got header containing the specified pattern
+    # 
+    # @warning this method is called extractPattern in pyRepet.seq.BioseqDB
+    #
+    # @param pattern regular expression of wished Bioseq header
+    # @param sourceBioseqDB the BioseqDB from which we want extract Bioseq
+    #
+    def addBioseqFromABioseqDBIfHeaderContainPattern(self, pattern, sourceBioseqDB):
+        if pattern=="" :
+            return
+        srch=re.compile(pattern)
+        for seq in sourceBioseqDB.db:
+            m=srch.search(seq.header)
+            if m:
+                self.add(seq)   
+                
+                
+    ## Up-case the sequence characters in all sequences
+    # 
+    def upCase( self ):
+        for bs in self.db:
+            bs.upCase()
+            
+            
+    ## Split each gapped Bioseq in a list and store all in a dictionary
+    #
+    # @return a dict, keys are bioseq headers, values are list of Map instances 
+    #
+    def getDictOfLMapsWithoutGaps( self ):
+        dSeq2Maps = {}
+
+        for bs in self.db:
+            dSeq2Maps[ bs.header ] = bs.getLMapWhithoutGap()
+
+        return dSeq2Maps
+
+    ## Give the list of the sequence length in the bank
+    #
+    # @return an list
+    #
+    def getListOfSequencesLength( self ):
+        lLength = []
+        for iBioseq in self.db:
+            lLength.append(iBioseq.getLength())
+
+        return lLength
+    
+    ## Return sequence length for a list of sequence header
+    #
+    def getSeqLengthByListOfName( self, lHeaderName ):
+        lseqLength=[]
+        for headerName in lHeaderName: 
+            lseqLength.append(self.getSeqLength( headerName ))
+        return lseqLength