diff smart_toolShed/commons/core/seq/BioseqUtils.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/seq/BioseqUtils.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,296 @@
+# 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 math
+import re
+from commons.core.seq.Bioseq import Bioseq
+
+## Static methods for sequences manipulation
+#
+class BioseqUtils(object):
+    
+    ## Translate a nucleotide sequence
+    #
+    # @param bioSeqInstanceToTranslate a bioseq instance to translate
+    # @param phase a integer : 1 (default), 2 or 3
+    # 
+    def translateSequence(bioSeqInstanceToTranslate, phase=1):
+        pep = ""
+        #length = math.floor((len(self.sequence)-phase-1)/3)*3
+        length = int( math.floor( ( len(bioSeqInstanceToTranslate.sequence )-( phase-1 ) )/3 )*3 )
+        #We need capital letters !
+        bioSeqInstanceToTranslate.upCase() 
+        sequence = bioSeqInstanceToTranslate.sequence                
+        for i in xrange(phase-1,length,3):
+            if (sequence[i:i+3] == "TTT" or sequence[i:i+3] == "TTC"):
+                pep = pep + "F"
+            elif ( sequence[i:i+3] == "TTA" or sequence[i:i+3] == "TTG" ):
+                pep = pep + "L"
+            elif ( sequence[i:i+2] == "CT" ):
+                pep = pep + "L"
+            elif ( sequence[i:i+3] == "ATT" or sequence[i:i+3] == "ATC" or sequence[i:i+3] == "ATA" ):
+                pep = pep + "I"
+            elif ( sequence[i:i+3] == "ATG" ):
+                pep = pep + "M"
+            elif ( sequence[i:i+2] == "GT" ):
+                pep = pep + "V"
+            elif ( sequence[i:i+2] == "TC" ) :
+                pep = pep + "S"
+            elif ( sequence[i:i+2] == "CC" ) :
+                pep = pep + "P"
+            elif ( sequence[i:i+2] == "AC" ) :
+                pep = pep + "T"
+            elif ( sequence[i:i+2] == "GC" ) :
+                pep = pep + "A"
+            elif ( sequence[i:i+3] == "TAT" or sequence[i:i+3] == "TAC" ) :
+                pep = pep + "Y"
+            elif ( sequence[i:i+3] == "TAA" or sequence[i:i+3] == "TAG" ) :
+                pep = pep + "*"
+            elif ( sequence[i:i+3] == "CAT" or sequence[i:i+3] == "CAC" ) :
+                pep = pep + "H"
+            elif ( sequence[i:i+3] == "CAA" or sequence[i:i+3] == "CAG" ) :
+                pep = pep + "Q"
+            elif ( sequence[i:i+3] == "AAT" or sequence[i:i+3] == "AAC" ) :
+                pep = pep + "N"
+            elif ( sequence[i:i+3] == "AAA" or sequence[i:i+3] == "AAG" ) :
+                pep = pep + "K"
+            elif ( sequence[i:i+3] == "GAT" or sequence[i:i+3] == "GAC" ) :
+                pep = pep + "D"
+            elif ( sequence[i:i+3] == "GAA" or sequence[i:i+3] == "GAG" ) :
+                pep = pep + "E"
+            elif ( sequence[i:i+3] == "TGT" or sequence[i:i+3] == "TGC" ) :
+                pep = pep + "C"
+            elif ( sequence[i:i+3] == "TGA" ) :
+                pep = pep + "*"
+            elif ( sequence[i:i+3] == "TGG" ) :
+                pep = pep + "W"
+            elif ( sequence[i:i+2] == "CG" ) :
+                pep = pep + "R"
+            elif ( sequence[i:i+3] == "AGT" or sequence[i:i+3] == "AGC" ) :
+                pep = pep + "S"
+            elif ( sequence[i:i+3] == "AGA" or sequence[i:i+3] == "AGG" ) :
+                pep = pep + "R"
+            elif ( sequence[i:i+2] == "GG" ):
+                pep = pep + "G"
+            #We don't know the amino acid because we don't have the nucleotide
+            #R      Purine (A or G)
+            #Y      Pyrimidine (C, T, or U)
+            #M      C or A
+            #K      T, U, or G
+            #W      T, U, or A
+            #S      C or G
+            #B      C, T, U, or G (not A)
+            #D      A, T, U, or G (not C)
+            #H      A, T, U, or C (not G)
+            #V      A, C, or G (not T, not U)
+            #N      Unknown nucleotide
+            elif ( re.search("N|R|Y|M|K|W|S|B|D|H|V", sequence[i:i+3])):
+                pep = pep + "X"                      
+        bioSeqInstanceToTranslate.sequence = pep
+        
+    translateSequence = staticmethod(translateSequence)
+    
+    ## Add the frame info in header
+    #
+    # @param bioSeqInstance a bioseq instance to translate
+    # @param phase a integer : 1 , 2 or 3
+    # 
+    def setFrameInfoOnHeader(bioSeqInstance, phase):
+        if " " in bioSeqInstance.header:
+            name, desc = bioSeqInstance.header.split(" ", 1)
+            name = name + "_" + str(phase)
+            bioSeqInstance.header = name + " " + desc
+        else:
+            bioSeqInstance.header = bioSeqInstance.header + "_" + str(phase)
+            
+    setFrameInfoOnHeader = staticmethod(setFrameInfoOnHeader)
+    
+    ## Translate a nucleotide sequence for all frames (positives and negatives)
+    #
+    # @param bioSeqInstanceToTranslate a bioseq instance to translate
+    #
+    def translateInAllFrame( bioSeqInstanceToTranslate ):
+        positives = BioseqUtils._translateInPositiveFrames( bioSeqInstanceToTranslate )        
+        negatives = BioseqUtils._translateInNegativeFrames( bioSeqInstanceToTranslate )         
+        listAll6Frames = []
+        listAll6Frames.extend(positives)
+        listAll6Frames.extend(negatives)
+        return listAll6Frames
+            
+    translateInAllFrame = staticmethod(translateInAllFrame)
+    
+    ## Replace the stop codons by X in sequence
+    #
+    # @param bioSeqInstance a bioseq instance
+    #
+    def replaceStopCodonsByX( bioSeqInstance ):
+        bioSeqInstance.sequence = bioSeqInstance.sequence.replace ("*", "X")
+            
+    replaceStopCodonsByX = staticmethod(replaceStopCodonsByX)  
+
+    ## Translate in a list all the frames of all the bioseq of bioseq list
+    #
+    # @param bioseqList a list of bioseq instances
+    # @return a list of translated bioseq instances
+    #
+    def translateBioseqListInAllFrames( bioseqList ):
+        bioseqListInAllFrames = []
+        for bioseq in bioseqList :
+            bioseqListInAllFrames.extend(BioseqUtils.translateInAllFrame(bioseq))
+        return bioseqListInAllFrames
+    
+    translateBioseqListInAllFrames = staticmethod( translateBioseqListInAllFrames )
+    
+    ## Replace the stop codons by X for each sequence of a bioseq list
+    #
+    # @param lBioseqWithStops a list of bioseq instances
+    # @return a list of bioseq instances
+    #
+    def replaceStopCodonsByXInBioseqList ( lBioseqWithStops ):
+        bioseqListWithStopsreplaced = []
+        for bioseq in lBioseqWithStops:
+            BioseqUtils.replaceStopCodonsByX(bioseq)
+            bioseqListWithStopsreplaced.append(bioseq)            
+        return bioseqListWithStopsreplaced
+    
+    replaceStopCodonsByXInBioseqList = staticmethod( replaceStopCodonsByXInBioseqList )
+    
+    ## Write a list of bioseq instances in a fasta file (60 characters per line)
+    #
+    # @param lBioseq a list of bioseq instances
+    # @param fileName string
+    #
+    def writeBioseqListIntoFastaFile( lBioseq, fileName ):
+        fout = open(fileName, "w")
+        for bioseq in lBioseq:
+                bioseq.write(fout)       
+        fout.close()
+    
+    writeBioseqListIntoFastaFile = staticmethod( writeBioseqListIntoFastaFile )
+    
+    ## read in a fasta file and create a list of bioseq instances
+    #
+    # @param fileName string
+    # @return a list of bioseq
+    #
+    def extractBioseqListFromFastaFile( fileName ):
+        file = open( fileName )
+        lBioseq = []
+        currentHeader = ""
+        while currentHeader != None:
+            bioseq = Bioseq()
+            bioseq.read(file)
+            currentHeader = bioseq.header
+            if currentHeader != None:
+                lBioseq.append(bioseq)
+        return lBioseq
+    
+    extractBioseqListFromFastaFile = staticmethod( extractBioseqListFromFastaFile )
+    
+    ## Give the length of a sequence search by name
+    #
+    # @param lBioseq a list of bioseq instances
+    # @param seqName string
+    # @return an integer
+    #
+    def getSeqLengthWithSeqName( lBioseq, seqName ):
+        length = 0
+        for bioseq in lBioseq:
+            if bioseq.header == seqName:
+                length = bioseq.getLength()
+                break        
+        return length
+
+    getSeqLengthWithSeqName = staticmethod( getSeqLengthWithSeqName )
+
+    def _translateInPositiveFrames( bioSeqInstanceToTranslate ):
+        seq1 = bioSeqInstanceToTranslate.copyBioseqInstance()
+        BioseqUtils.setFrameInfoOnHeader(seq1, 1)
+        BioseqUtils.translateSequence(seq1, 1)
+        seq2 = bioSeqInstanceToTranslate.copyBioseqInstance()
+        BioseqUtils.setFrameInfoOnHeader(seq2, 2)
+        BioseqUtils.translateSequence(seq2, 2)
+        seq3 = bioSeqInstanceToTranslate.copyBioseqInstance()
+        BioseqUtils.setFrameInfoOnHeader(seq3, 3)
+        BioseqUtils.translateSequence(seq3, 3)
+        return [seq1, seq2, seq3]
+    
+    _translateInPositiveFrames = staticmethod( _translateInPositiveFrames )
+    
+    def _translateInNegativeFrames(bioSeqInstanceToTranslate):
+        seq4 = bioSeqInstanceToTranslate.copyBioseqInstance()
+        seq4.reverseComplement()
+        BioseqUtils.setFrameInfoOnHeader(seq4, 4)
+        BioseqUtils.translateSequence(seq4, 1)
+        seq5 = bioSeqInstanceToTranslate.copyBioseqInstance()
+        seq5.reverseComplement()
+        BioseqUtils.setFrameInfoOnHeader(seq5, 5)
+        BioseqUtils.translateSequence(seq5, 2)
+        seq6 = bioSeqInstanceToTranslate.copyBioseqInstance()
+        seq6.reverseComplement()
+        BioseqUtils.setFrameInfoOnHeader(seq6, 6)
+        BioseqUtils.translateSequence(seq6, 3)
+        return [seq4, seq5, seq6]
+    
+    _translateInNegativeFrames = staticmethod( _translateInNegativeFrames )
+    
+    
+    ## Return a dictionary which keys are sequence headers and values sequence lengths.
+    #
+    def getLengthPerSeqFromFile( inFile ):
+        dHeader2Length = {}
+        inFileHandler = open( inFile, "r" )
+        while True:
+            iBs = Bioseq()
+            iBs.read( inFileHandler )
+            if iBs.sequence == None:
+                break
+            dHeader2Length[ iBs.header ] = iBs.getLength()
+        inFileHandler.close()
+        return dHeader2Length
+    
+    getLengthPerSeqFromFile = staticmethod( getLengthPerSeqFromFile )
+    
+    
+    ## Return the list of Bioseq instances, these being sorted in decreasing length
+    #
+    def getBioseqListSortedByDecreasingLength( lBioseqs ):
+        return sorted( lBioseqs, key=lambda iBs: ( iBs.getLength() ), reverse=True )
+    
+    getBioseqListSortedByDecreasingLength = staticmethod( getBioseqListSortedByDecreasingLength )
+    
+    
+    ## Return the list of Bioseq instances, these being sorted in decreasing length (without gaps)
+    #
+    def getBioseqListSortedByDecreasingLengthWithoutGaps( lBioseqs ):
+        return sorted( lBioseqs, key=lambda iBs: ( len(iBs.sequence.replace("-","")) ), reverse=True )
+    
+    getBioseqListSortedByDecreasingLengthWithoutGaps = staticmethod( getBioseqListSortedByDecreasingLengthWithoutGaps )