diff TEisotools-1.1.a/commons/core/seq/BioseqDB.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/commons/core/seq/BioseqDB.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,494 +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.
-
-
-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