diff TEisotools-1.0/TEiso/ClosestToStartSite.py @ 6:20ec0d14798e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/TEiso/ClosestToStartSite.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,333 @@
+#!/usr/bin/env python
+
+# 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.
+
+from commons.core.LoggerFactory             import LoggerFactory
+from commons.core.utils.RepetOptionParser   import RepetOptionParser
+from commons.core.checker.RepetException    import RepetException
+from commons.core.utils.FileUtils           import FileUtils
+import re,os
+LOG_NAME = "TEiso"
+
+class ClosestToStartSite(object):
+    
+    def __init__(self, inputFile = "", cuffcom_tmap =   "", outputFile = "", verbosity = 3):
+        self._inputFile = inputFile
+        self._cuffcom_tmap = cuffcom_tmap
+        self._outputFile = outputFile
+        self._verbosity = verbosity
+        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_NAME, self.__class__.__name__), self._verbosity)
+            
+    def setAttributesFromCmdLine(self):
+        self._toolVersion = "1.0"
+        description = "ClosestToStartSite version %s" % self._toolVersion
+        epilog = "\nParser a bed file and create a bed file to create a report about positions of features A to features B. \n"
+        epilog +="it can also add the class code of features A.\n"
+        epilog += "example: ClosestToStartSite.py -i <inputFile> -c <cuff_in.tmap> -o <outputFile>\n"
+        parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "input bed file name.",  default = "")
+        parser.add_option("-c", "--cuffcom_tmap",  dest = "cuffcom_tmap",  action = "store", type = "string", help = "input gtf file of cuffcompare (<cuff_in>.tmap)",  default = "")
+        parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output file name", default = "")
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "verbosity [optional] [default: 3]",default = 3)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._inputFile  = options.inputFile
+        self._cuffcom_tmap = options.cuffcom_tmap
+        self._outputFile = options.outputFile
+        self._verbosity  = options.verbosity
+                    
+    def _logAndRaise(self, errorMsg):
+        self._log.error(errorMsg)
+        raise RepetException(errorMsg)
+
+    def checkoption(self):
+        if self._inputFile == "":
+            self._log.info("Missing input file")
+        else:
+            if not FileUtils.isRessourceExists(self._inputFile):
+                self._log.info("'%s' doesn't exist!" % self._inputFile)	
+
+        if self._cuffcom_tmap != "":
+            if not FileUtils.isRessourceExists(self._cuffcom_tmap):
+                self._log.info("'%s' doesn't exist!" % self._cuffcom_tmap)
+	    if self._outputFile == "":
+		self._outputFile = "%s_Close2TSS_with_classcode.bed" % os.path.splitext(self._inputFile)[0]
+    	    else:
+           	if FileUtils.isRessourceExists(self._outputFile):
+                	self._log.info("Output file '%s' already exists!" % self._outputFile)
+        else:
+           if self._outputFile == "":
+                self._outputFile = "%s_Close2TSS.bed" % os.path.splitext(self._inputFile)[0]
+           else:
+           	if FileUtils.isRessourceExists(self._outputFile):
+                	self._log.info("Output file '%s' already exists!" % self._outputFile)
+		
+            
+    def getClassCodeCuffcompare(self, tmap_file, listPossitions):
+        class_code_dic = {}
+        lcode_ref = []
+        tmp = []
+        linetowrite =[]
+        with open(tmap_file) as tmap:
+                tmapline = tmap.readlines()
+                for i in range(1,len(tmapline)):
+                    cuff_id = tmapline[i].split("\t")[4].strip()
+                    class_code = tmapline[i].split("\t")[2].strip()
+                    ref_id = tmapline[i].split("\t")[1].strip()
+                    lcode_ref.append(class_code)
+                    lcode_ref.append(ref_id)
+                    class_code_dic[cuff_id] = lcode_ref
+                    lcode_ref = []
+        
+        
+        for i in xrange(0,len(listPossitions)):
+            tmp.extend(listPossitions[i])
+            transcript_bedtools = listPossitions[i][3]
+                
+            if transcript_bedtools in class_code_dic.keys():
+                    tmp.append(class_code_dic[transcript_bedtools][0])
+                    tmp.append(class_code_dic[transcript_bedtools][1])
+            else:
+                    tmp.append("NA")
+                    tmp.append("NA")
+            linetowrite.append(tmp)
+            tmp=[]
+        return linetowrite
+        
+
+           
+    def getClosestToStartSite(self, inputFile):
+        linelist = []
+        tmplist = []
+        with open(inputFile, "r") as bedFile:
+            for line in bedFile.readlines():
+                m = re.search(r"^\s*(\S+)\t+(\d+)\t+(\d+)\t+([^\t]+)\t+([^\t]+)\t+([+-])\t+(\d+\.\d+)\t+([^\t]+)+\t+(\d+)\t+(\d+)\t+([^\t]+)+\t+([^\t]+)\t+([+-])\t+([^\t]+)",line)
+                if(m != None):
+                    start_TR = int(m.group(2))##F[1]
+                    end_TR = int(m.group(3))##F[2]
+                    strand_TR= m.group(6) ##[5]
+                    start_TE = int(m.group(9))##[8]
+                    end_TE = int(m.group(10))##[9]
+                    dist = int(m.group(14))##[13]
+                    if (start_TE < start_TR) and (end_TE < start_TR) and (strand_TR =="+") and (end_TR > end_TE) and (end_TR > start_TE) and (dist != 0):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(line.split("\t")[13].strip())
+                        tmplist.append("TE_closest_TSS")
+                        linelist.append(tmplist)
+                        tmplist = []
+            #                        F[1]   gene             F[2]
+            #                        =========================>
+            #         ------------
+            #        F[8]        F[9]
+    
+                    if (start_TE > end_TR) and (end_TE > end_TR) and (strand_TR =="-") and (start_TR < start_TE) and (start_TR < end_TE) and (dist != 0):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(line.split("\t")[13].strip())
+                        tmplist.append("TE_closest_TSS")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                        F[1]                F[2]
+            #                        <======================
+            #                                                    ---------------
+                  
+                    if (start_TE <= start_TR) and (start_TR < end_TE) and (strand_TR =="+") and (end_TR > end_TE) and (end_TR > start_TE):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        overlap = (end_TE-start_TR)+1
+                        tmplist.append(overlap)
+                        tmplist.append("TE_overlap_TSS")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                        F[1]   gene             F[2]
+            #                        =========================>
+            #                 -------------
+            #                F[8]        F[9]
+            
+            #                                         gene
+            #                                F[1]=========================>F[2]
+            
+            #                                F[8]---------------F[9]
+            
+            
+                    if (start_TE < start_TR) and (start_TR == end_TE) and (strand_TR =="+") and (end_TR > end_TE) and (end_TR > start_TE):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        tmplist.append("TE_overlap_TSS")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            ##                                F[1]=============================>F[2]
+            ##                 F[8]---------------F[9]
+            
+            
+                    if (start_TE < end_TR) and (end_TR <= end_TE) and (strand_TR =="-") and (start_TR < start_TE) and (start_TR < end_TE):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        overlap = (end_TR-start_TE)+1
+                        tmplist.append(overlap)
+                        tmplist.append("TE_overlap_TSS")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            
+            #                        F[1]<======================F[2]
+            #                                           ---------------
+            #                                        F[8]           F[9]
+            #
+            #
+            #                    F[1]<=============================F[2]
+            #                                   F[8]---------------F[9]
+            
+                    if (start_TE == end_TR) and (end_TR < end_TE) and (strand_TR =="-") and (start_TR < start_TE) and (start_TR < end_TE):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        tmplist.append("TE_overlap_TSS")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                                                F[1]<=============================F[2]
+            #                                                                                F[8]---------------F[9]
+            
+                    if (start_TR < start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE < end_TR) and (dist == 0):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        #tmplist.append(line.strip())
+                        tmplist.append("TE_in_gene")
+                        linelist.append(tmplist)
+                        tmplist = []
+                  
+            
+            #                        F[1]            gene          F[2]
+            #                        ==============================
+            #                                 -----------
+            #                                F[8]        F[9]
+            
+            
+                    if (start_TE < start_TR) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TR < end_TE):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        #lenTE = (end_TE-start_TE)+1
+                        tmplist.append(0)
+                        tmplist.append("gene_in_TE")
+                        linelist.append(tmplist)
+                        tmplist = []
+                        
+            #                        F[1]======================F[2]
+            #        F[8]----------------------------------------------------F[9]
+            
+            
+                    if (strand_TR =="+") and (start_TR > start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE == end_TR):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        #tmplist.append(line.strip())
+                        tmplist.append("gene_in_TE")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                                                                F[1]==================================>F[2]
+            #                                        F[8]----------------------------------------------------------F[9]
+            
+                    if (strand_TR =="-") and (start_TR > start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE == end_TR):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        #tmplist.append(line.strip())
+                        tmplist.append("gene_in_TE")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                                                                F[1]<==================================F[2]
+            #                                        F[8]----------------------------------------------------------F[9]
+            
+                    if (strand_TR =="+") and (start_TR == start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE > end_TR):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        #tmplist.append(line.strip())
+                        tmplist.append("gene_in_TE")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                                                                F[1]==================================>F[2]
+            #                                                                F[8]----------------------------------------------------------F[9]
+            
+                    if (strand_TR =="-") and (start_TR == start_TE) and (start_TR < end_TE) and (start_TE < end_TR) and (end_TE > end_TR):
+                        for i in range(0,len(line.split("\t"))-1):
+                            tmplist.append(line.split("\t")[i])
+                        tmplist.append(0)
+                        #tmplist.append(line.strip())
+                        tmplist.append("gene_in_TE")
+                        linelist.append(tmplist)
+                        tmplist = []
+            
+            #                                                                F[1]<==================================F[2]
+            #                                                                F[8]----------------------------------------------------------F[9]
+        
+        return linelist
+    
+    
+    def writeOutputFromList(self, listPossitions , outputFile):
+        w = open(outputFile,'w')
+        for s in listPossitions:
+            line= "\t".join(str(item) for item in s)
+            w.write("%s\n" % line)
+        w.close()
+
+                
+    def run(self):
+        self.checkoption()
+        listPossitions = self.getClosestToStartSite(self._inputFile)
+        if self._cuffcom_tmap == "":
+            self.writeOutputFromList(listPossitions, self._outputFile )
+        else:
+            listclasscode = self.getClassCodeCuffcompare(self._cuffcom_tmap, listPossitions)
+            self.writeOutputFromList(listclasscode, self._outputFile)
+                
+if __name__== "__main__":
+    iClosestToStartSite = ClosestToStartSite()
+    iClosestToStartSite.setAttributesFromCmdLine()
+    iClosestToStartSite.run()
+
+
+
+
+
+