diff smart_toolShed/commons/core/parsing/BlatToGffForBesPaired.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/parsing/BlatToGffForBesPaired.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,266 @@
+# 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 optparse
+import os
+import sys
+import re
+import datetime
+from commons.core.parsing.BlatParser import BlatParser
+from commons.core.seq.FastaUtils import FastaUtils 
+
+class BlatToGffForBesPaired(object):
+
+
+    def __init__(self):
+        pass
+    
+    def setAttributesFromCmdLine(self):
+        help = '\
+        \nThis Script Launch BlatToGffForBesPaired.\n\n\
+        Example 1: python BlatToGffForBesPaired.py -i blatResultsFile.tab -f besSequences.fasta -o outputFile.gff3\n\
+        Example 2: python BlatToGffForBesPaired.py -i blatResultsFile.tab -f besSequences.fasta -o outputFile.gff3 -n muscadine:filtre1\n\n\
+        Note 1: In blat input file, all BAC-Ends must be paired. In addition, they must be one above the other.\nFor example, if you have the BES MRRE1H032F08FM1 (forward), we must have the BES MRRE1H032F08RM1 (reverse) just after, like:\n\
+        554\t26\t0\t0\t1\t16\t1\t17\t+\tMRRE1H032F08FM1\t606\t10\t606\tchr11\t19818926\t3725876\t3726473\t2\t553,27,\t10,579,\t3725876,3726446,\n\
+        620\t23\t0\t0\t0\t0\t0\t0\t-\tMRRE1H032F08RM1\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n\
+        Note 2: the header in Blat results output file must be present (5 lines).\n\n'
+                
+        parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
+        parser.add_option( '-i', '--input', dest='inputBLAT', help='Blat Input File Name, with BES paired (1 Forward and 1 Reverse) [Format: tabular]', default= None )
+        parser.add_option( '-f', '--fasta', dest='inputFASTA', help='Fasta Input File Name, with all sequences of BES [Format: fasta]', default= None )
+        parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
+        parser.add_option( '-n', '--methodname', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
+        ( options, args ) = parser.parse_args()
+        self._options = options
+    
+    def checkOptions(self):
+        if self._options.inputBLAT == '':
+            raise Exception("ERROR: No Blat file specified for -i !")
+        elif not os.path.exists(self._options.inputBLAT):
+            raise Exception("ERROR: Blat Input File doesn't exist !")
+        else:
+            self._inputFileBlat = self._options.inputBLAT
+            
+        if self._options.inputFASTA == '':
+            raise Exception("ERROR: No Fasta file specified for -f !")
+        elif not os.path.exists(self._options.inputFASTA):
+            raise Exception("ERROR: Fasta Input File doesn't exist !")
+        else:
+            self._inputFileFasta = self._options.inputFASTA
+            
+        if self._options.output == '':
+            raise Exception("ERROR: No Output file specified for -o !")
+        else:
+            self._outputFileGFF = self._options.output
+            
+        self._methodName = self._options.methodName
+            
+    def run(self):
+        self.checkOptions()
+        self._createGFFOutputFile()
+        BLATFile = open(self._inputFileBlat, 'r')
+        
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        blatLine = BLATFile.readline()
+        numberLine = 6
+        while blatLine != '':
+            lGffLines = []
+            
+            gffLineBes1, besName1, seqBes1, typeBes1 = self.convertBlatObjectToGffLine(blatLine, numberLine)
+            lGffLines.append(gffLineBes1)
+            
+            blatLine = BLATFile.readline()
+            numberLine = numberLine + 1
+            
+            gffLineBes2, besName2, seqBes2, typeBes2 = self.convertBlatObjectToGffLine(blatLine, numberLine)
+            lGffLines.append(gffLineBes2)
+            
+            gffLineBac = self.createGffLineForBac(gffLineBes1, besName1, seqBes1, typeBes1, gffLineBes2, besName2, seqBes2, typeBes2, numberLine)
+            lGffLines.append(gffLineBac)
+            
+            if gffLineBac != None:
+                self._printGFFLinesToOutputFile(lGffLines)
+                
+            blatLine = BLATFile.readline()
+            numberLine = numberLine + 1
+            
+    def convertBlatObjectToGffLine(self, blatLine, numberLine):
+        iBlatHit = BlatParser()
+        iBlatHit.setAttributesFromString(blatLine, numberLine)
+        besName = iBlatHit.getQName()
+        seqBes = self.extractBesSequenceFromFastaFile(besName, numberLine)
+        
+        typeBes = ''
+        if re.match('^.+FM[0-9]$', besName):
+            typeBes = 'FM'
+        elif re.match('^.+RM[0-9]$', besName):
+            typeBes = 'RM'
+        
+        col1 = iBlatHit.getTName()
+        col2 = 'BlatToGffForBesPaired'
+        if self._methodName == '' or self._methodName == None:
+            col3 = 'BES'
+        else:
+            col3 = '%s:BES' % self._methodName
+        col4 = iBlatHit.getTStart()
+        col5 = iBlatHit.getTEnd()
+        col6 = '.'
+        col7 = '+'
+        col8 = '.'
+        col9 = 'ID=%s;Name=%s;bes_start=%s;bes_end=%s;bes_size=%s;muscadine_seq=%s' % (besName, besName, iBlatHit.getTStart(), iBlatHit.getTEnd(), iBlatHit.getTSize(), seqBes)
+            
+        gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
+        return gffLine, iBlatHit.getQName(),seqBes, typeBes
+    
+    def createGffLineForBac(self, gffLineBes1, besName1, seqBes1, typeBes1, gffLineBes2, besName2, seqBes2, typeBes2, numberLine):
+        lGffLineBes1 = gffLineBes1.split('\t')
+        lGffLineBes2 = gffLineBes2.split('\t')
+        besName1 = self.getBesName(lGffLineBes1[8])
+        besName2 = self.getBesName(lGffLineBes2[8])
+        
+        tBes1 = (lGffLineBes1[0], int(lGffLineBes1[3]), int(lGffLineBes1[4]))
+        tBes2 = (lGffLineBes2[0], int(lGffLineBes2[3]), int(lGffLineBes2[4]))
+        
+        if self.checkBesNames(besName1, besName2, numberLine) == True and self.checkBesPositions(tBes1, tBes2) == True:
+            startBacPos, endBacPos = self.getBacPositions(tBes1, tBes2)
+            sizeBacPos = endBacPos - startBacPos + 1
+            bacName = self.getBacName(besName1)
+            nameBesFM, seqBesFM, nameBesRM, seqBesRM = self.getBesFmAndRmNamesAndSequences(besName1, seqBes1, typeBes1, besName2, seqBes2, typeBes2)
+            
+            col1 = lGffLineBes1[0]
+            col2 = 'BlatToGffForBesPaired'
+            if self._methodName == '' or self._methodName == None:
+                col3 = 'BAC'
+            else:
+                col3 = '%s:BAC' % self._methodName
+            col4 = startBacPos
+            col5 = endBacPos
+            col6 = '.'
+            col7 = '.'
+            col8 = '.'
+            col9 = 'ID=%s;Name=%s;bac_start=%s;bac_end=%s;bac_size=%s;besFM_name=%s;muscadine_besFM_seq=%s;besRM_name=%s;muscadine_besRM_seq=%s' % (bacName, bacName, startBacPos, endBacPos, sizeBacPos, nameBesFM, seqBesFM, nameBesRM, seqBesRM)
+            gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
+            return gffLine
+        return None
+    
+    def getBesFmAndRmNamesAndSequences(self, besName1, seqBes1, typeBes1, besName2, seqBes2, typeBes2):
+        if typeBes1 == 'FM' and typeBes2 == 'RM':
+            return besName1, seqBes1, besName2, seqBes2
+        elif typeBes1== 'RM' and typeBes2 == 'FM':
+            return besName2, seqBes2, besName1, seqBes1
+
+    def getBesName(self, col9):
+        lCol9 = col9.split(';')
+        ID = lCol9[0]
+        besName = ID[3:]
+        return besName
+    
+    def getBacName(self, besName):
+        bacName = besName[:-3]
+        return bacName
+
+    def checkBesNames(self, besName1, besName2, line):
+        bacName1 = besName1[:-3]
+        bacName2 = besName2[:-3]
+        if bacName1 == bacName2:
+            return True
+        else:
+            sys.stderr.write("WARNING: Lines %s and %s the two Bes (%s AND %s) do not belong to the same BAC !!!\n  -> you have to filter this Blat file...\n" % (int(line)-1, line, besName1, besName2))
+            return False
+    
+    def checkBesPositions(self, tBes1, tBes2):
+        if tBes1[0] == tBes2[0]:
+            minBes1 = min(tBes1[1], tBes1[2])
+            maxBes1 = max(tBes1[1], tBes1[2])
+            minBes2 = min(tBes2[1], tBes2[2])
+            maxBes2 = max(tBes2[1], tBes2[2])
+            if (minBes1 < minBes2 and maxBes1 < minBes2) or (minBes2 < minBes1 and maxBes2 < minBes1):
+                return True
+        return False
+    
+    def getBacPositions(self, tBes1, tBes2):
+        startBacPos = 0
+        endBacPos = 0
+        minBes1 = min(tBes1[1], tBes1[2])
+        maxBes1 = max(tBes1[1], tBes1[2])
+        minBes2 = min(tBes2[1], tBes2[2])
+        maxBes2 = max(tBes2[1], tBes2[2])
+        if minBes1 < minBes2:
+            startBacPos = minBes1
+            endBacPos = maxBes2
+        else:
+            startBacPos = minBes2
+            endBacPos = maxBes1
+        return startBacPos, endBacPos
+    
+    def extractBesSequenceFromFastaFile(self, besName, numberLine):
+        seq = ''
+        date = datetime.datetime.now()
+        date = date.strftime("%d%m%Y_%H%M%S")
+        tmpFileName = 'tmp_BlatToGffForBesPaired_%s.fasta' % date
+        iFastaUtils = FastaUtils()
+        iFastaUtils.dbExtractByPattern(besName, self._inputFileFasta, tmpFileName)
+        
+        if os.path.exists(tmpFileName):
+            newFastaFile = open(tmpFileName, 'r')
+            line = newFastaFile.readline()
+            if line != '':
+                while line != '':
+                    if line[0] != '>':
+                        line = line.replace('\n', '')
+                        seq += line
+                    line = newFastaFile.readline()
+                newFastaFile.close()
+                os.remove(tmpFileName)
+                return seq
+            os.remove(tmpFileName)
+        
+        sys.stderr.write("WARNING: At line %s, the BAC-Ends (%s) hasn't got sequence in fasta file (%s) !!\n" % (numberLine, besName, os.path.basename(self._inputFileFasta)))
+        return 'NA'
+    
+    def _createGFFOutputFile(self):
+        GFFfile = open(self._outputFileGFF, 'w')
+        GFFfile.write("##gff-version 3\n")
+        GFFfile.close()
+        
+    def _printGFFLinesToOutputFile(self, lLines):
+        GFFfile = open(self._outputFileGFF, 'a')
+        for line in lLines:
+            GFFfile.write(line)
+        GFFfile.close()
+
+if __name__ == '__main__':
+    iBlatToGffForBesPaired = BlatToGffForBesPaired()
+    iBlatToGffForBesPaired.setAttributesFromCmdLine()
+    iBlatToGffForBesPaired.run()
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