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

Uploaded

--- a/TEisotools-1.1.a/commons/core/utils/ClassifUtils.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,311 +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 os
-import json
-from collections import OrderedDict
-from commons.tools.RenameHeaderClassif import RenameHeaderClassif
-
-class ClassifUtils(object):
-    
-    @staticmethod
-    def _formatProfilesResultsAsDict(lProfilesResults):
-        if len(lProfilesResults) == 0:
-            return OrderedDict()
-
-        dResults = OrderedDict()
-
-        for refNameAndCoverage in lProfilesResults:
-            refName, coverage = refNameAndCoverage.split(": ")
-
-            coverage = coverage.split("%(")
-            coverageOnSubject = float(coverage.pop(1).replace("%)", ""))
-            coverage = float(coverage.pop(0))
-
-            profilesResult = OrderedDict()
-            profilesResult["cov"] = coverage
-            profilesResult["covOnSubject"] = coverageOnSubject
-            dResults[refName] = profilesResult
-        return dResults
-    
-    @staticmethod    
-    def _formatCodingFeaturesAsDict(lineOfEvidence, dCoding):
-        codingEvidences = lineOfEvidence.split("; ")
-
-        for codingTypeData in codingEvidences:
-            codingTypeData = codingTypeData.split(": ")
-            codingType = codingTypeData.pop(0)
-
-            codingTypeData = ": ".join(codingTypeData)
-            codingTypeData = codingTypeData.split(", ")
-
-            if codingType == "TE_BLRtx":
-                if not dCoding.has_key("TE_BLRtx"):
-                    dCoding["TE_BLRtx"] = OrderedDict()
-                for refNameAndCoverage in codingTypeData:
-                    blrtxResult = OrderedDict()
-                    refName, coverage = refNameAndCoverage.rsplit(": ", 1)
-                    coverage = float(coverage.replace("%", ""))
-                    blrtxResult["cov"] = coverage
-                    dCoding["TE_BLRtx"][refName] = blrtxResult
-
-            if codingType == "TE_BLRx":
-                if not dCoding.has_key("TE_BLRx"):
-                    dCoding["TE_BLRx"] = OrderedDict()
-                for refNameAndCoverage in codingTypeData:
-                    blrxResult = OrderedDict()
-                    refName, coverage = refNameAndCoverage.rsplit(": ", 1)
-                    coverage = float(coverage.replace("%", ""))
-                    blrxResult["cov"] = coverage
-                    dCoding["TE_BLRx"][refName] = blrxResult
-
-            if codingType == "profiles":
-                dCoding["profiles"] = ClassifUtils._formatProfilesResultsAsDict(codingTypeData)
-
-            if codingType == "Other_profiles":
-                dCoding["Other_profiles"] = ClassifUtils._formatProfilesResultsAsDict(codingTypeData)
-
-            if codingType == "rDNA_BLRn":
-                dCoding["rDNA_BLRn"] = OrderedDict()
-                codingTypeData = ", ".join(codingTypeData)
-                try:
-                    refName, coverage = codingTypeData.rsplit(": ", 1)
-                    coverage = float(coverage.replace("%", ""))
-                except ValueError:
-                    refName = codingTypeData
-                    coverage = -1.0
-
-                dCoding["rDNA_BLRn"]["name"] = refName
-                dCoding["rDNA_BLRn"]["cov"] = coverage
-
-            if codingType == "HG_BLRn":
-                dCoding["HG_BLRn"] = OrderedDict()
-                refName, coverage = codingTypeData[0].rsplit(": ", 1)
-                coverage = float(coverage.replace("%", ""))
-
-                dCoding["HG_BLRn"]["name"] = refName
-                dCoding["HG_BLRn"]["cov"] = coverage
-    
-    @staticmethod
-    def _formatStructFeaturesAsDict(lineOfEvidence, dStruct):
-        structEvidences = lineOfEvidence.split("; ")
-        for structTypeData in structEvidences:
-
-            structTypeData = structTypeData.split(": ")
-            structType = structTypeData.pop(0)
-
-            structTypeData = ": ".join(structTypeData)
-            structTypeData = structTypeData.split(", ")
-
-            if structType == "TElength":
-                dStruct["TElength"] = structTypeData.pop()
-
-            if structType == "TermRepeats":
-                dStruct["TermRepeats"] = OrderedDict()
-                for refNameAndLength in structTypeData:
-                    refName, length = refNameAndLength.rsplit(": ", 1)
-                    dStruct["TermRepeats"][refName] = int(length)
-
-            if structType == "ORF":
-                if not dStruct.has_key("ORF"):
-                    dStruct["ORF"] = structTypeData
-
-            if structType in ["SSR", "SSRtrf"]:
-                if not dStruct.has_key(structType):
-                    dStruct[structType] = structTypeData
-
-            if "SSRCoverage" in structType :
-                dummy, cov = structType.split("=")
-                dStruct["SSRCoverage"] = float(cov)
-
-            if structType == "polyAtail":
-                dStruct["polyAtail"] = True
-
-            if structType == "helitronExtremities":
-                structTypeData = ", ".join(structTypeData)
-                structTypeData = structTypeData.split("), ")
-                dStruct["helitronExtremities"] = OrderedDict()
-                for helitronData in structTypeData:
-                    helName, helData = helitronData.split(": (")
-                    helData = helData.replace(")", "")
-                    eValue, start, end = helData.split(", ")
-
-                    helitronExtResult = OrderedDict()
-                    helitronExtResult["start"] = int(start)
-                    helitronExtResult["end"] = int(end)
-                    helitronExtResult["eValue"] = float(eValue)
-                    dStruct["helitronExtremities"][helName] = helitronExtResult
-    
-    @staticmethod
-    def _formatOtherFeaturesAsDict(lineOfEvidence, dOther):
-        if lineOfEvidence != "":
-            ClassifUtils._formatCodingFeaturesAsDict(lineOfEvidence, dOther)
-            ClassifUtils._formatStructFeaturesAsDict(lineOfEvidence, dOther)
-    
-    @staticmethod
-    def getClassifLineAsDict(line):
-        dClassif = OrderedDict()
-        iRenameHeaderClassif = RenameHeaderClassif()
-        lClassifItem = line.split("\t")
-        if len(lClassifItem) != 8:
-            msg = "Can't parse line: \"%s\"\n" % line.strip()
-            print("WARNING - ClassifUtils - %s" % msg)
-            return dClassif
-        
-        teClass = lClassifItem[4]
-        teOrder = lClassifItem[5]
-        # TODO: recompute wicker code like this or force the user to provide a classif file as input with the wicker code already added
-        wCode = iRenameHeaderClassif._decisionRuleForWickerCode(teClass, teOrder)
-        
-        dClassif["name"] = lClassifItem[0]
-        dClassif["wCode"] = wCode
-        dClassif["length"] = int(lClassifItem[1])
-        dClassif["strand"] = lClassifItem[2]
-        dClassif["chimeric"] = False if lClassifItem[3] == "ok" else True
-        
-        dClassif["class"] = teClass
-        dClassif["order"] = teOrder
-        
-        if(lClassifItem[6] == "complete"):
-            dClassif["complete"] = True
-        elif(lClassifItem[6] == "incomplete"):
-            dClassif["complete"] = False
-        else:
-            dClassif["complete"] = None
-
-        allFields = lClassifItem[7].split("; ")
-        
-        CI = allFields.pop(0)
-        CI = CI.split("=")[-1]
-        if CI != "NA":
-            try:
-                CI = int(CI)
-            except ValueError as e:
-                print "Couldn't convert %s to int : %s" % (CI, e)
-        dClassif["CI"] = CI
-        
-        dClassif["coding"] = OrderedDict()
-        dClassif["struct"] = OrderedDict()
-        dClassif["other"] = OrderedDict()
-        
-        allFields = "; ".join(allFields)
-        codingField = ""
-        structField = ""
-        otherField = ""
-        
-        codingStart = allFields.find("coding=(")
-        if codingStart != -1:
-            pCount = 1
-            trueStart = codingStart + len("coding=(")
-            end = trueStart
-            for char in allFields[trueStart:]:
-                if char == "(":
-                    pCount += 1
-                if char == ")":
-                    pCount -= 1
-                if pCount == 0:
-                    break;
-                end += 1
-            if pCount == 0:
-                codingField = allFields[trueStart:end]
-        
-        structStart = allFields.find("struct=(")
-        if structStart != -1:
-            pCount = 1
-            trueStart = structStart + len("struct=(")
-            end = trueStart
-            for char in allFields[trueStart:]:
-                if char == "(":
-                    pCount += 1
-                if char == ")":
-                    pCount -= 1
-                if pCount == 0:
-                    break;
-                end += 1
-            structField = allFields[trueStart:end]
-            
-        otherStart = allFields.find("other=(")
-        if otherStart != -1:
-            pCount = 1
-            trueStart = otherStart + len("other=(")
-            end = trueStart
-            for char in allFields[trueStart:]:
-                if char == "(":
-                    pCount += 1
-                if char == ")":
-                    pCount -= 1
-                if pCount == 0:
-                    break;
-                end += 1
-            otherField = allFields[trueStart:end]
-        
-        if codingField != "":
-            ClassifUtils._formatCodingFeaturesAsDict(codingField, dClassif["coding"])
-        if structField != "":
-            ClassifUtils._formatStructFeaturesAsDict(structField, dClassif["struct"])
-        if otherField != "":
-            ClassifUtils._formatOtherFeaturesAsDict(otherField, dClassif["other"])
-
-        return dClassif
-    
-    ## Retrieve the classification informations of a classif file
-    # 
-    # @param fileName Name of the classif file
-    # @return A dict containing the classification infos
-    #
-    @staticmethod
-    def getClassifInfosAsDict(fileName):
-        dConsensusInfo = OrderedDict()
-
-        ext = os.path.splitext(fileName)[1]
-        if  ext != ".classif":
-            msg = "Input file must be a classif file from TEdenovo\n"
-            print("ERROR - ClassifUtils - %s" % msg)
-            exit(1)
-        
-        with open(fileName, "r") as classifFile:
-            for line in classifFile:
-                seqName = line.split("\t")[0]
-                dConsensusInfo[seqName] = ClassifUtils.getClassifLineAsDict(line)
-        
-        return dConsensusInfo
-    
-    ## Convert a classif file to JSON format
-    # 
-    # @param fileName Name of the classif file
-    # @param outFileName Name of the output JSON file (optional)
-    #  
-    @staticmethod
-    def convertClassifToJson(fileName, outFileName = ""):
-        dConsensusInfo = ClassifUtils.getClassifInfosAsDict(fileName)
-        if outFileName == "":
-            outFileName = "%s_classif.json" % (os.path.basename(fileName).rsplit(".", 1)[0])
-        with open(outFileName, 'w') as outFile:
-            json.dump(dConsensusInfo, outFile)