#!/usr/bin/env python
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"""This script defines FastaBasedAlignService, a subclass of AlignService,
which converts PacBio reads in BASE/PULSE/FOFN formats into FASTA format before
align."""

# Author: Yuan Li
from __future__ import absolute_import
from pbalign.alignservice.align import AlignService
from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS
from pbcore.util.Process import backticks
import logging


class FastaBasedAlignService(AlignService):
    """An abstract class for aligners that do not support PacBio reads in
    BASE/PULSE/FOFN formats. All subclasses need to call _pls2fasta in
    preprocess to convert input PacBio reads to FASTA."""

    def _pls2fasta(self, inputFileName, regionTable, noSplitSubreads):
        """ Call pls2fasta to convert a PacBio BASE/PULSe/FOFN file to FASTA.
            Input:
                inputFilieName : a PacBio BASE/PULSE/FOFN file.
                regionTable    : a region table RGN.H5/FOFN file.
                noSplitSubreads: whether to split subreads or not.
            Output:
                a FASTA file which can be used as an input by an aligner.
        """
        # If the incoming file is a FASTA file, no conversion is needed.
        if getFileFormat(inputFileName) == FILE_FORMATS.FASTA:
            return inputFileName

        # Otherwise, create a temporary FASTA file to write.
        outFastaFile = self._tempFileManager.RegisterNewTmpFile(
            suffix=".fasta")

        cmdStr = "pls2fasta {plsFile} {fastaFile} ".format(
            plsFile=inputFileName, fastaFile=outFastaFile)

        if regionTable is not None and regionTable != "":
            cmdStr += " -regionTable {rt} ".format(rt=regionTable)

        if noSplitSubreads:
            cmdStr += " -noSplitSubreads "

        logging.info(self.name + ": Convert {inFile} to FASTA format.".
                     format(inFile=inputFileName))
        logging.debug(self.name + ": Call \"{cmd}\"".format(cmd=cmdStr))

        _output, errCode, errMsg = backticks(cmdStr)
        if errCode != 0:
            errMsg += "Failed to convert {i} to {o}.".format(
                      i=inputFileName, o=outFastaFile)
            logging.error(errMsg)
            raise RuntimeError(errMsg)

        # Return the converted FASTA file which can be used by an aligner.
        return outFastaFile