Esempio n. 1
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 def test_realpath(self):
     """Test real_upath and real_ppath."""
     print real_upath("ref with space")
     self.assertTrue(real_upath("ref with space").endswith("ref\ with\ space"))
     self.assertTrue(real_upath("ref\ with\ space").endswith("ref\ with\ space"))
     self.assertTrue(real_ppath("ref with space").endswith("ref with space"))
     self.assertTrue(real_ppath("ref\ with\ space").endswith("ref with space"))
Esempio n. 2
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    def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
        """Generate a SAM, BAM or a CMP.H5 file.
        Input:
            inSam   : an input SAM/BAM file. (e.g. fileName.filteredSam)
            refFile : the reference file. (e.g. fileName.targetFileName)
            outFile : the output SAM/BAM or CMP.H5 file.
                      (i.e. fileName.outputFileName)
            readType: standard or cDNA or CCS (can be None if not specified)
        Output:
            output, errCode, errMsg
        """
        output, errCode, errMsg = "", 0, ""

        outFormat = getFileFormat(outFile)

        if outFormat == FILE_FORMATS.BAM:
            pass  # Nothing to be done
        if outFormat == FILE_FORMATS.SAM:
            logging.info("OutputService: Genearte the output SAM file.")
            logging.debug("OutputService: Move {src} as {dst}".format(
                src=inSam, dst=outFile))
            try:
                shutil.move(real_ppath(inSam), real_ppath(outFile))
            except shutil.Error as e:
                output, errCode, errMsg = "", 1, str(e)
        elif outFormat == FILE_FORMATS.CMP:
            #`samtoh5 inSam outFile -readType readType
            logging.info("OutputService: Genearte the output CMP.H5 " +
                         "file using samtoh5.")
            prog = "samtoh5"
            cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
                samFile=inSam, refFile=refFile, outFile=outFile)
            if readType is not None:
                cmd += " -readType {0} ".format(readType)
            if smrtTitle:
                cmd += " -smrtTitle "
            # Execute the command line
            logging.debug("OutputService: Call \"{0}\"".format(cmd))
            output, errCode, errMsg = backticks(cmd)
        elif outFormat == FILE_FORMATS.XML:
            logging.info(
                "OutputService: Generating the output XML file".format(
                    samFile=inSam, outFile=outFile))
            # Create {out}.xml, given {out}.bam
            outBam = str(outFile[0:-3]) + "bam"
            aln = None
            # FIXME This should really be more automatic
            if self.args.readType == "CCS":
                self._output_dataset_type = ConsensusAlignmentSet
            aln = self._output_dataset_type(real_ppath(outBam))
            for res in aln.externalResources:
                res.reference = refFile
            aln.write(outFile)

        if errCode != 0:
            errMsg = prog + " returned a non-zero exit status." + errMsg
            logging.error(errMsg)
            raise RuntimeError(errMsg)
        return output, errCode, errMsg
Esempio n. 3
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    def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
        """Generate a SAM, BAM or a CMP.H5 file.
        Input:
            inSam   : an input SAM/BAM file. (e.g. fileName.filteredSam)
            refFile : the reference file. (e.g. fileName.targetFileName)
            outFile : the output SAM/BAM or CMP.H5 file.
                      (i.e. fileName.outputFileName)
            readType: standard or cDNA or CCS (can be None if not specified)
        Output:
            output, errCode, errMsg
        """
        output, errCode, errMsg = "", 0, ""

        outFormat = getFileFormat(outFile)

        if outFormat == FILE_FORMATS.BAM:
            pass # Nothing to be done
        if outFormat == FILE_FORMATS.SAM:
            logging.info("OutputService: Genearte the output SAM file.")
            logging.debug("OutputService: Move {src} as {dst}".format(
                src=inSam, dst=outFile))
            try:
                shutil.move(real_ppath(inSam), real_ppath(outFile))
            except shutil.Error as e:
                output, errCode, errMsg = "", 1, str(e)
        elif outFormat == FILE_FORMATS.CMP:
            #`samtoh5 inSam outFile -readType readType
            logging.info("OutputService: Genearte the output CMP.H5 " +
                         "file using samtoh5.")
            prog = "samtoh5"
            cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
                samFile=inSam, refFile=refFile, outFile=outFile)
            if readType is not None:
                cmd += " -readType {0} ".format(readType)
            if smrtTitle:
                cmd += " -smrtTitle "
            # Execute the command line
            logging.debug("OutputService: Call \"{0}\"".format(cmd))
            output, errCode, errMsg = backticks(cmd)
        elif outFormat == FILE_FORMATS.XML:
            logging.info("OutputService: Generating the output XML file".
                         format(samFile=inSam, outFile=outFile))
            # Create {out}.xml, given {out}.bam
            outBam = str(outFile[0:-3]) + "bam"
            aln = None
            # FIXME This should really be more automatic
            if self.args.readType == "CCS":
                self._output_dataset_type = ConsensusAlignmentSet
            aln = self._output_dataset_type(real_ppath(outBam))
            for res in aln.externalResources:
                res.reference = refFile
            aln.write(outFile)

        if errCode != 0:
            errMsg = prog + " returned a non-zero exit status." + errMsg
            logging.error(errMsg)
            raise RuntimeError(errMsg)
        return output, errCode, errMsg
Esempio n. 4
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 def test_realpath(self):
     """Test real_upath and real_ppath."""
     print real_upath("ref with space")
     self.assertTrue(
         real_upath("ref with space").endswith("ref\ with\ space"))
     self.assertTrue(
         real_upath("ref\ with\ space").endswith("ref\ with\ space"))
     self.assertTrue(
         real_ppath("ref with space").endswith("ref with space"))
     self.assertTrue(
         real_ppath("ref\ with\ space").endswith("ref with space"))
Esempio n. 5
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    def _output(self, inSam, refFile, outFile, readType=None):
        """Generate a SAM, BAM file.
        Input:
            inSam   : an input SAM/BAM file. (e.g. fileName.filteredSam)
            refFile : the reference file. (e.g. fileName.targetFileName)
            outFile : the output SAM/BAM file
                      (i.e. fileName.outputFileName)
            readType: standard or cDNA or CCS (can be None if not specified)
        Output:
            output, errCode, errMsg
        """
        output, errCode, errMsg = "", 0, ""

        outFormat = getFileFormat(outFile)

        if outFormat == FILE_FORMATS.BAM:
            pass  # Nothing to be done
        if outFormat == FILE_FORMATS.SAM:
            logging.info("OutputService: Genearte the output SAM file.")
            logging.debug("OutputService: Move %s as %s", inSam, outFile)
            try:
                shutil.move(real_ppath(inSam), real_ppath(outFile))
            except shutil.Error as e:
                output, errCode, errMsg = "", 1, "Exited with error: " + str(e)
                logging.error(errMsg)
                raise RuntimeError(errMsg)
        elif outFormat == FILE_FORMATS.CMP:
            errMsg = "pbalign no longer supports CMP.H5 Output in 3.0."
            logging.error(errMsg)
            raise IOError(errMsg)
        elif outFormat == FILE_FORMATS.XML:
            logging.info("OutputService: Generating the output XML file %s %s",
                         inSam, outFile)
            # Create {out}.xml, given {out}.bam
            outBam = str(outFile[0:-3]) + "bam"
            aln = None
            # FIXME This should really be more automatic
            if readType == "CCS":
                self._output_dataset_type = ConsensusAlignmentSet
            aln = self._output_dataset_type(real_ppath(outBam))
            for res in aln.externalResources:
                res.reference = refFile
            aln.write(outFile)

        return output, errCode, errMsg
Esempio n. 6
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    def _output(self, inSam, refFile, outFile, readType=None):
        """Generate a SAM, BAM file.
        Input:
            inSam   : an input SAM/BAM file. (e.g. fileName.filteredSam)
            refFile : the reference file. (e.g. fileName.targetFileName)
            outFile : the output SAM/BAM file
                      (i.e. fileName.outputFileName)
            readType: standard or cDNA or CCS (can be None if not specified)
        Output:
            output, errCode, errMsg
        """
        output, errCode, errMsg = "", 0, ""

        outFormat = getFileFormat(outFile)

        if outFormat == FILE_FORMATS.BAM:
            pass # Nothing to be done
        if outFormat == FILE_FORMATS.SAM:
            logging.info("OutputService: Genearte the output SAM file.")
            logging.debug("OutputService: Move %s as %s", inSam, outFile)
            try:
                shutil.move(real_ppath(inSam), real_ppath(outFile))
            except shutil.Error as e:
                output, errCode, errMsg = "", 1, "Exited with error: " + str(e)
                logging.error(errMsg)
                raise RuntimeError(errMsg)
        elif outFormat == FILE_FORMATS.CMP:
            errMsg = "pbalign no longer supports CMP.H5 Output in 3.0."
            logging.error(errMsg)
            raise IOError(errMsg)
        elif outFormat == FILE_FORMATS.XML:
            logging.info("OutputService: Generating the output XML file %s %s",
                         inSam, outFile)
            # Create {out}.xml, given {out}.bam
            outBam = str(outFile[0:-3]) + "bam"
            aln = None
            # FIXME This should really be more automatic
            if readType == "CCS":
                self._output_dataset_type = ConsensusAlignmentSet
            aln = self._output_dataset_type(real_ppath(outBam))
            for res in aln.externalResources:
                res.reference = refFile
            aln.write(outFile)

        return output, errCode, errMsg
Esempio n. 7
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    def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
        """Generate a sam or a cmp.h5 file.
        Input:
            inSam   : an input SAM file. (e.g. fileName.filteredSam)
            refFile : the reference file. (e.g. fileName.targetFileName)
            outFile : the output SAM or CMP.H5 file.
                      (i.e. fileName.outputFileName)
            readType: standard or cDNA or CCS (can be None if not specified)
        Output:
            output, errCode, errMsg
        """
        output, errCode, errMsg = "", 0, ""

        if getFileFormat(outFile) == FILE_FORMATS.SAM:
            #`mv inSam outFile`
            logging.info("OutputService: Genearte the output SAM file.")
            logging.debug("OutputService: Move {src} as {dst}".format(
                src=inSam, dst=outFile))
            try:
                shutil.move(real_ppath(inSam), real_ppath(outFile))
            except shutil.Error as e:
                output, errCode, errMsg = "", 1, str(e)
        elif getFileFormat(outFile) == FILE_FORMATS.CMP:
            #`samtoh5 inSam outFile -readType readType
            logging.info("OutputService: Genearte the output CMP.H5 " +
                         "file using samtoh5.")
            prog = "samtoh5"
            cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
                samFile=inSam, refFile=refFile, outFile=outFile)
            if readType is not None:
                cmd += " -readType {0} ".format(readType)
            if smrtTitle:
                cmd += " -smrtTitle "
            # Execute the command line
            logging.debug("OutputService: Call \"{0}\"".format(cmd))
            output, errCode, errMsg = backticks(cmd)

        if errCode != 0:
            errMsg = prog + " returned a non-zero exit status." + errMsg
            logging.error(errMsg)
            raise RuntimeError(errMsg)
        return output, errCode, errMsg