Python GenericTsvReader.getComments方法代碼示例

# 需要導入模塊: from oncotator.utils.GenericTsvReader import GenericTsvReader [as 別名]
# 或者: from oncotator.utils.GenericTsvReader.GenericTsvReader import getComments [as 別名]
    def testTCGAMAFAsInputAndQuickAnnotate(self):
        """ Test that we can take in a TCGA MAF (using MAFLITE), do annotating, and still render it properly """
        inputFilename = "testdata/maf/Patient0.maf.annotated"
        tmp = MafliteInputMutationCreator(inputFilename, 'configs/maflite_input.config')
        outputFilename = "out/testTCGAMAFAsInputAndQuickAnnotate.tsv"
        outputRenderer = TcgaMafOutputRenderer(outputFilename, 'configs/tcgaMAF2.4_output.config')
        annotator = Annotator()
        
        annotator.setInputCreator(tmp)
        annotator.setOutputRenderer(outputRenderer)
        ds = DatasourceFactory.createDatasource("testdata/thaga_janakari_gene_ds/hg19/tj_data.config", "testdata/thaga_janakari_gene_ds/hg19/")
        annotator.addDatasource(ds)
        annotator.annotate()
        
        statinfo = os.stat(outputFilename)
        self.assertTrue(statinfo.st_size > 0, "Generated MAF file (" + outputFilename + ") is empty.")
        tsvReaderIn = GenericTsvReader(inputFilename)
        tsvReader = GenericTsvReader(outputFilename)
        
        self.assertTrue(tsvReader.getComments().find('#version') != -1, "First line did not specify a version number")
        self.assertTrue("i_TJ_Data_Why" in tsvReader.getFieldNames(), "New field missing (i_TJ_Data_Why) from header")
        self.assertTrue("i_TJ_Data_Who" in tsvReader.getFieldNames(), "New field missing (i_TJ_Data_Who) from header")
        
        ctrOut = 0
        for lineDict in tsvReader:
            ctrOut += 1
        ctrIn = 0
        for lineDict in tsvReaderIn:
            ctrIn += 1
        ctrIn += len(tsvReaderIn.getCommentsAsList())
        ctrOut += len(tsvReader.getCommentsAsList())

        self.assertTrue(ctrOut == (ctrIn + 2), "Output file should have same number of lines plus two (for maf version and Oncotator version comments) as input file.  (In,Out): " + str(ctrIn) + ", " + str(ctrOut))

# 需要導入模塊: from oncotator.utils.GenericTsvReader import GenericTsvReader [as 別名]
# 或者: from oncotator.utils.GenericTsvReader.GenericTsvReader import getComments [as 別名]
    def sortFile(self, filename, func, length=50000):
        """
        This method sorts the input file and writes out the sorted file to filename.

        :param filename: sorted filename
        :param func: function that converts each row of the input file to an unique, sortable key
        :param length: maximum number of lines in a partition
        """
        reader = GenericTsvReader(filename=self.readfilename, commentPrepend=self.commentPrepend,
                                  delimiter=self.delimiter)
        comments = reader.getComments()

        fieldnames = reader.getFieldNames()
        if fieldnames is None:
            fieldnames = []

        fieldnameIndexes = collections.OrderedDict()
        if fieldnames is not None:
            fieldnameIndexes = collections.OrderedDict([(x, i) for (i, x) in enumerate(fieldnames)])

        iterable = iter(reader.getInputContentFP())
        partitions = self._yieldPartitions(iterable, func, fieldnameIndexes, length)

        with open(name=filename, mode='wb', buffering=64 * 1024) as writer:
            writer.write(comments)
            writer.write(string.join(fieldnames, self.delimiter) + "\n")
            writer.writelines(self._merge(partitions))  # generators are allowed as inputs to writelines function

# 需要導入模塊: from oncotator.utils.GenericTsvReader import GenericTsvReader [as 別名]
# 或者: from oncotator.utils.GenericTsvReader.GenericTsvReader import getComments [as 別名]
    def _validateTcgaMafContents(self, filename):
        """ This is a utility, private method for unit tests to get a semblance that a valid maf file was created.  
        
        Note: This method has nothing to do with the TCGA validator.
        
        """
        configFile = ConfigUtils.createConfigParser(os.path.join("configs", "tcgaMAF2.4_output.config"))
        statinfo = os.stat(filename)
        self.assertTrue(statinfo.st_size > 0, "Generated MAF file (" + filename + ") is empty.")

        tsvReader = GenericTsvReader(filename)

        self.assertTrue(tsvReader.getComments().find('#version') != -1, "First line did not specify a version number")

        ctr = 1
        for lineDict in tsvReader:

            # TODO: Re-enable when GENCODE and HGNC datasources are concordant (or Entrez_Gene_ID is in the gencode gtf)
            # if lineDict['Entrez_Gene_Id'] == "0":
            #     self.assertTrue(lineDict['Hugo_Symbol'] == "Unknown", "Entrez_Gene_Id was zero, but Hugo Symbol was not 'Unknown'.  Line: " + str(ctr))

            unknownKeys = []
            self.assertTrue(lineDict["Tumor_Seq_Allele1"] != lineDict["Tumor_Seq_Allele2"], "Reference and alternate were equal in TCGA MAF output on line %d (%s)" % (ctr, lineDict["Tumor_Seq_Allele1"]))
            self.assertTrue(lineDict["Tumor_Seq_Allele1"] == lineDict["Reference_Allele"], "Reference Allele should match Tumor_Seq_Allele1 on line " + str(ctr))
            uniprot_aa_xform_counter = 0
            for k in lineDict.keys():
                if lineDict[k] == "__UNKNOWN__":
                    unknownKeys.append(k)

                self.assertTrue('\r' not in lineDict[k], "Carriage return character found in an annotation value.")

                requiredColumns = configFile.get("general", "requiredColumns")
                optionalColumns = configFile.get("general", "optionalColumns")
                exposedColumns = configFile.get("general", "exposedColumns")
                if (k not in requiredColumns) and (k not in optionalColumns) and (k not in exposedColumns):
                    self.assertTrue(k.startswith("i_"), "Internal column was not prepended with 'i_'")
            if lineDict['UniProt_AApos'] == "0":
                uniprot_aa_xform_counter += 1

            if lineDict["Variant_Type"] == VariantClassification.VT_DEL:
                self.assertTrue(lineDict["Tumor_Seq_Allele2"] == "-")

            if lineDict["Variant_Type"] == VariantClassification.VT_INS:
                self.assertTrue(lineDict["Reference_Allele"] == "-")

            unknownKeys.sort()
            self.assertTrue(len(unknownKeys) == 0, "__UNKNOWN__ values (" + str(len(unknownKeys)) + ") seen on line " + str(ctr) + ", in fields: " + ", ".join(unknownKeys))
            self.assertTrue(uniprot_aa_xform_counter < 10, "Too many uniprot aa xform values are zero (" + str(uniprot_aa_xform_counter) + ").  This is probably an error.")

            ctr += 1

# 需要導入模塊: from oncotator.utils.GenericTsvReader import GenericTsvReader [as 別名]
# 或者: from oncotator.utils.GenericTsvReader.GenericTsvReader import getComments [as 別名]
    def _validateTcgaMafContents(self, filename):
        """
        This is a utility, private method for unit tests to get a semblance that a valid maf file was created.
        
        Note: This method has nothing to do with the TCGA validator.
        
        TODO: This is code duplication from TCGA MAF Output RendererTest.  This should be refactored into a base class
        (to preserve self.assertTrue, etc).
        """
        statinfo = os.stat(filename)
        self.assertTrue(statinfo.st_size > 0, "Generated MAF file (" + filename + ") is empty.")

        tsvReader = GenericTsvReader(filename)

        self.assertTrue(tsvReader.getComments().find('#version') <> -1, "First line did not specify a version number")

        ctr = 1
        for lineDict in tsvReader:
            if lineDict['Entrez_Gene_Id'] == "0":
                self.assertTrue(lineDict['Hugo_Symbol'] == "Unknown",
                                "Entrez_Gene_Id was zero, but Hugo Symbol was not 'Unknown'.  Line: " + str(ctr))

            unknownKeys = []
            for k in lineDict.keys():
                if lineDict[k] == "__UNKNOWN__":
                    unknownKeys.append(k)

                self.assertTrue('\r' not in lineDict[k], "Carriage return character found in an annotation value.")

                configFile = ConfigUtils.createConfigParser('configs/tcgaMAF2.3_output.config')
                requiredColumns = configFile.get("general", "requiredColumns")
                optionalColumns = configFile.get("general", "optionalColumns")
                if (k not in requiredColumns) and (k not in optionalColumns):
                    self.assertTrue(k.startswith("i_"), "Internal column was not prepended with 'i_'")

            unknownKeys.sort()
            self.assertTrue(len(unknownKeys) == 0,
                            "__UNKNOWN__ values (" + str(len(unknownKeys)) + ") seen on line " + str(
                                ctr) + ", in fields: " + ", ".join(unknownKeys))

            ctr += 1