Source code for bioconvert.bam2fasta

###########################################################################
# Bioconvert is a project to facilitate the interconversion               #
# of life science data from one format to another.                        #
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# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
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"""Convert :term:`BAM` format to :term:`FASTA` format"""
import os
import subprocess

from bioconvert import ConvBase
from bioconvert.core.decorators import requires
from bioconvert.core.utils import get_extension


class BAM2FASTA(ConvBase):
    """Convert sorted :term:`BAM` file into :term:`FASTA` file

    Methods available are based on samtools [SAMTOOLS]_ or bedtools [BEDTOOLS]_.

    .. warning:: Using the bedtools method, the R1 and R2 reads must be next to
        each other so that the reads are sorted similarly

    .. warning:: there is no guarantee that the R1/R2 output file are sorted
        similarly in paired-end case due to supp and second reads

    """

    #: Default value
    _default_method = "samtools"

    def __init__(self, infile, outfile):
        """.. rubric:: constructor

        :param str infile: BAM file
        :param str outfile: FASTA file

        """
        super(BAM2FASTA, self).__init__(infile, outfile)

    """@requires("bamtools")
    def __method_bamtools(self, *args, **kwargs):
        #  fastq are split on several lines (80 characters)
        # this method contains supplementary reads and we don't know
        # what to do with them for now. So, this method is
        # commented. Indeed final R1 and R2 files will not be paired.

        cmd = "bamtools stats -in '%s' | sed '12!d' | awk '{print $3}' " % (self.infile)
        ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
            stderr=subprocess.STDOUT,universal_newlines=True)
        isPaired = ps.communicate()[0].strip()

        # Collect the extension
        ext = os.path.splitext(self.outfile)[1]

        cmd = "bamtools convert -format fasta -in {} -out {}".format(
            self.infile, self.outfile)
        self.execute(cmd)
   """

    @requires("samtools")
    def _method_samtools(self, *args, **kwargs):
        """
        do the conversion :term:`BAM` -> :term:`FASTA` using samtools.

        .. note:: fasta are on one line

        `SAMtools documentation <http://www.htslib.org/doc/samtools.html>`_"""
        # Test if input bam file is paired
        p = subprocess.Popen(
            "samtools view -c -f 1 {}".format(self.infile).split(),
            stdout=subprocess.PIPE,
            stderr=subprocess.PIPE,
            universal_newlines=True,
        )

        isPaired = p.communicate()[0].strip()

        # Collect the extension
        ext = os.path.splitext(self.outfile)[1]

        # FIXME: this compression code may be factorised ?

        output_ext = get_extension(self.outfile, remove_compression=True)

        # If the output file extension is compress extension
        if ext in [".gz", ".bz2"]:
            outbasename = os.path.splitext(self.outfile)[0].split(".", 1)[0]

            if ext == ".gz":
                compresscmd = "gzip -f"
            elif ext == ".bz2":
                compresscmd = "pbzip2 -f"

            # When the input file is not paired and the output file needs to be compressed
            if isPaired == "0":
                cmd = "samtools fasta {} > {}.{}".format(self.infile, outbasename, output_ext)
                self.execute(cmd)
                cmd = "{} {}.{}".format(compresscmd, outbasename, output_ext)
                self.execute(cmd)
            # When the input file is paired and the output file needs to be compressed
            else:
                cmd = "samtools fasta -1 {}_1.{} -2 {}_2.{} -n {} ".format(
                    outbasename, output_ext, outbasename, output_ext, self.infile
                )
                self.execute(cmd)
                cmd = "{} {}_1.{}".format(compresscmd, outbasename, output_ext)
                self.execute(cmd)
                cmd = "{} {}_2.{}".format(compresscmd, outbasename, output_ext)
                self.execute(cmd)
        else:
            outbasename = os.path.splitext(self.outfile)[0]

            # When the input file is not paired
            if isPaired == "0":
                cmd = "samtools fasta {} > {}".format(self.infile, self.outfile)
                self.execute(cmd)
            # When the input file is paired
            else:
                cmd = "samtools fasta -1 {}_1.{} -2 {}_2.{} -n {} ".format(
                    outbasename, output_ext, outbasename, output_ext, self.infile
                )
                self.execute(cmd)