bioconvert 1.2.0__py3-none-any.whl

bioconvert/__init__.py

@@ -0,0 +1,74 @@
+__version__ = "1.2.0"
+try:
+    from importlib.metadata import version as _get_version, PackageNotFoundError
+    version = _get_version("bioconvert")
+except PackageNotFoundError:
+    version = __version__
+
+import os
+
+import colorlog
+
+# This will create a HOME/.config/bioconvert where files (e.g., executables)
+# can be downloaded
+from easydev import CustomConfig
+
+configuration = CustomConfig("bioconvert", verbose=True)
+
+os.environ["GOPATH"] = os.environ["HOME"] + "/go"
+os.environ["PATH"] = os.environ["GOPATH"] + "/bin/:" + os.environ["PATH"]
+
+from easydev.logging_tools import Logging
+
+logger = Logging("bioconvert", "INFO")
+
+
+def bioconvert_script(filename, where=None):
+    bioconvert_path = bioconvert.__path__[0]
+    share = os.path.join(bioconvert_path, "misc")
+    if where:
+        filename = os.path.join(share, where, filename)
+    else:
+        filename = os.path.join(share, filename)
+    if not os.path.exists(filename):
+        raise FileNotFoundError("unknown file {}".format(filename))
+    return filename
+
+
+def bioconvert_data(filename, where=None):
+    """Simple utilities to retrieve data sets from bioconvert/data directory
+
+    :param str filename: the name of the data file to get the path
+    :param str where:
+    """
+    bioconvert_path = bioconvert.__path__[0]
+    share = os.path.join(bioconvert_path, "data")
+    # in the code one may use / or \
+    if where:
+        filename = os.path.join(share, where, filename)
+    else:
+        filename = os.path.join(share, filename)
+    if not os.path.exists(filename):
+        raise FileNotFoundError("unknown file {}".format(filename))
+    return filename
+
+
+def info():
+    from bioconvert.core.registry import Registry
+
+    r = Registry()
+    info = r.get_info()
+    converters = [x for x in info.items()]
+    data = [info[k] for k, v in info.items()]
+    msg = "Bioconvert contains {} converters including {} methods"
+    return msg.format(len(converters), sum(data))
+
+
+import bioconvert
+from bioconvert.core.base import ConvBase
+from bioconvert.core.benchmark import Benchmark
+from bioconvert.core.converter import Bioconvert
+from bioconvert.core.decorators import compressor, requires
+from bioconvert.core.registry import Registry
+from bioconvert.core.shell import shell
+from bioconvert.core.utils import TempFile, md5

bioconvert/abi2fasta.py

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+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`ABI` format to :term:`FASTA` format"""
+from bioconvert import ConvBase, requires
+
+__all__ = ["ABI2FASTA"]
+
+
+class ABI2FASTA(ConvBase):
+    """Convert :term:`ABI` file to :term:`FASTQ` file
+
+    :term:`ABI` files are created by ABI sequencing machine and includes
+    PHRED quality scores for base calls. This allows the creation of
+    :term:`FastA` files.
+
+    Method implemented is based on BioPython [BIOPYTHON]_.
+
+    """
+
+    #: Default value
+    _default_method = "biopython"
+
+    def __init__(self, infile, outfile, *args, **kargs):
+        """.. rubric:: constructor
+
+        :param str infile: input ABI file
+        :param str outfile: output FASTA filename
+
+        """
+        super(ABI2FASTA, self).__init__(infile, outfile, *args, **kargs)
+
+    @requires(python_library="biopython")
+    def _method_biopython(self, *args, **kwargs):
+        """For this method we use the biopython package Bio.SeqIO.
+
+        :reference: `Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
+        from Bio import SeqIO
+
+        records = SeqIO.parse(self.infile, "abi")
+        SeqIO.write(records, self.outfile, "fasta")

bioconvert/abi2fastq.py

@@ -0,0 +1,60 @@
+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`ABI` format to :term:`FASTQ` format"""
+from bioconvert import ConvBase, requires
+
+__all__ = ["ABI2FASTQ"]
+
+
+class ABI2FASTQ(ConvBase):
+    """Convert :term:`ABI` file to :term:`FASTQ` file
+
+    :term:`ABI` files are created by ABI sequencing machine and includes
+    PHRED quality scores for base calls. This allows the creation
+    of :term:`FastQ` files.
+
+    Method implemented is based on BioPython [BIOPYTHON]_.
+    """
+
+    #: Default value
+    _default_method = "biopython"
+
+    def __init__(self, infile, outfile, *args, **kargs):
+        """.. rubric:: constructor
+
+        :param str infile: input ABI file
+        :param str outfile: output FASTQ filename
+
+        """
+        super(ABI2FASTQ, self).__init__(infile, outfile, *args, **kargs)
+
+    @requires(python_library="biopython")
+    def _method_biopython(self, *args, **kwargs):
+        """For this method we use the biopython package Bio.SeqIO.
+
+        `Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
+        from Bio import SeqIO
+
+        records = SeqIO.parse(self.infile, "abi")
+        SeqIO.write(records, self.outfile, "fastq")

bioconvert/abi2qual.py

@@ -0,0 +1,69 @@
+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`ABI` format to :term:`QUAL` format"""
+from bioconvert import ConvBase, requires
+
+__all__ = ["ABI2QUAL"]
+
+
+class ABI2QUAL(ConvBase):
+    """Convert :term:`ABI` file to :term:`QUAL` file
+
+    :term:`ABI` files are created by ABI sequencing machine and
+    includes PHRED quality scores for base calls. This allows
+    the creation of :term:`QUAL` files.
+
+    Method implemented is based on BioPython [BIOPYTHON]_.
+
+    """
+
+    #: Default value
+    _default_method = "biopython"
+
+    def __init__(self, infile, outfile, *args, **kargs):
+        """.. rubric:: constructor
+
+        :param str infile: input ABI file
+        :param str outfile: output QUAL filename
+
+        """
+        super(ABI2QUAL, self).__init__(infile, outfile, *args, **kargs)
+
+    @requires(python_library="biopython")
+    def _method_biopython(self, *args, **kwargs):
+        """For this method we use the biopython package Bio.SeqIO.
+
+        `Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
+        from Bio import SeqIO
+
+        records = SeqIO.parse(self.infile, "abi")
+        # output using SeqIO.write(records, self.outfile, "qual") is not
+        # standard so we write our own conversion here below
+        with open(self.outfile, "w") as fout:
+            for rec in records:
+                header = rec.name
+                qual = rec.letter_annotations["phred_quality"]
+                qual = "".join([str(x) for x in qual])
+                fout.write(">{}\n".format(header))
+                fout.write("{}\n".format(qual))

bioconvert/bam2bedgraph.py

@@ -0,0 +1,109 @@
+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`BAM` format to :term:`BEDGRAPH` format"""
+import colorlog
+
+from bioconvert import ConvBase
+from bioconvert.core.decorators import requires
+
+_log = colorlog.getLogger(__name__)
+
+
+__all__ = ["BAM2BEDGRAPH"]
+
+
+class BAM2BEDGRAPH(ConvBase):
+    """Convert sorted :term:`BAM` file into :term:`BEDGRAPH` file
+
+    Compute the coverage (depth) in BEDGRAPH.
+    Regions with zero coverage are also reported.
+
+
+    Note that this BEDGRAPH format is of the form::
+
+        chrom chromStart chromEnd dataValue
+
+    Note that consecutive positions with same values are compressed.
+
+    ::
+
+        chr1    0   75  0
+        chr1    75  176 1
+        chr1    176  177 2
+
+
+    .. warning:: the BAM file must be sorted. This can be achieved with
+        bamtools.
+
+
+    Methods available are based on bedtools [BEDTOOLS]_ and mosdepth
+    [MOSDEPTH]_.
+    """
+
+    # 4 minutes with bedtools and 20s with mosdepth
+    #: Default value
+    _default_method = "bedtools"
+    _threading = True
+
+    def __init__(self, infile, outfile):
+        """.. rubric:: Constructor
+
+        :param str infile: The path to the input BAM file.
+            **It must be sorted**.
+        :param str outfile: The path to the output file
+        """
+        super().__init__(infile, outfile)
+
+    @requires("bedtools")
+    def _method_bedtools(self, *args, **kwargs):
+        """Do the conversion using bedtools.
+
+        `bedtools documentation <https://bedtools.readthedocs.io/en/latest/>`_"""
+        cmd = "bedtools genomecov -bga -ibam {} > {}".format(self.infile, self.outfile)
+        self.execute(cmd)
+
+    @requires("mosdepth")
+    def _method_mosdepth(self, *args, **kwargs):
+        """Do the conversion using mosdepth.
+
+        `mosdepth documentation <https://github.com/brentp/mosdepth>`_"""
+        # For testing, we need to save into a specific temporary directory
+        import tempfile
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            try:
+                cmd = "mosdepth {}/.bioconvert -t {}  {}".format(tmpdir, self.threads, self.infile)
+                self.execute(cmd)
+
+                if self.outfile.endswith(".gz"):
+                    pass
+                else:
+                    cmd = "gunzip -c {}/.bioconvert.per-base.bed.gz > {}".format(tmpdir, self.outfile)
+                    self.execute(cmd)
+            except Exception as err:
+                raise (err)
+            finally:
+                cmd = "rm -f {name}/.bioconvert.per-base.bed.gz {name}/.bioconvert.per-base.bed.gz.csi"
+                cmd += " {name}/.bioconvert.mosdepth.global.dist.txt"
+                self.execute(cmd.format(name=tmpdir))

bioconvert/bam2bigwig.py

@@ -0,0 +1,98 @@
+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`BAM` file to :term:`BIGWIG` format"""
+
+import colorlog
+from tempfile import NamedTemporaryFile
+
+from bioconvert import ConvBase
+from bioconvert.core.base import ConvArg
+from bioconvert.core.decorators import requires
+
+_log = colorlog.getLogger(__name__)
+
+__all__ = ["BAM2BIGWIG"]
+
+
+class BAM2BIGWIG(ConvBase):
+    """Convert :term:`BAM` file to :term:`BIGWIG` file
+
+    Convert BAM into a binary version of :term:`WIG` format.
+
+    Methods are base on bamCoverage [DEEPTOOLS]_ and bedGraphToBigWig from
+    wiggletools [WIGGLETOOLS]_. Wiggletools method requires an extra argument
+    (--chrom-sizes) therefore default one is bamCoverage for now.
+
+    Moreover, the two methods do not return exactly the same info!
+
+    You can check this by using bioconvert to convert into a human readable file
+    such as wiggle. We will use the bamCoverage as our default conversion.
+
+    """
+
+    #: Default value
+    _default_method = "bamCoverage"
+
+    def __init__(self, infile, outfile, *args, **kargs):
+        """.. rubric:: constructor
+
+        :param str infile: input BAM file
+        :param str outfile: output BIGWIG filename
+
+        """
+        super(BAM2BIGWIG, self).__init__(infile, outfile, *args, **kargs)
+
+    @requires("bamCoverage")
+    def _method_bamCoverage(self, *args, **kwargs):
+        """run bamCoverage package.
+
+        `bamCoverage documentation <https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html>`_"""
+        cmd = "bamCoverage --bam {} --outFileFormat bigwig --outFileName {}".format(self.infile, self.outfile)
+        self.execute(cmd)
+
+    @requires(external_binaries=["bedGraphToBigWig", "bedtools"])
+    def _method_ucsc(self, *args, **kwargs):
+        """Run ucsc tool bedGraphToBigWig.
+
+        Requires extra argument (chrom_sizes) required by the bioconvert
+        standalone.
+        """
+        from bioconvert.bam2bedgraph import BAM2BEDGRAPH
+        from bioconvert.bedgraph2bigwig import BEDGRAPH2BIGWIG
+
+        chrom_sizes = kwargs.get("chrom_sizes", None)
+
+        with NamedTemporaryFile(suffix=".bedgraph") as fh:
+            convertbam2bed = BAM2BEDGRAPH(self.infile, fh.name)
+            convertbam2bed()
+            convertbed2bw = BEDGRAPH2BIGWIG(fh.name, self.outfile)
+            convertbed2bw(chrom_sizes=chrom_sizes)
+
+    @classmethod
+    def get_additional_arguments(cls):
+        yield ConvArg(
+            names="--chrom-sizes",
+            default=None,
+            help="a two-column file/URL: <chromosome name> <size in bases>. " "Used by the ucsc method only",
+        )

bioconvert/bam2cov.py

@@ -0,0 +1,81 @@
+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`BAM` format to :term:`COV` format"""
+import colorlog
+
+from bioconvert import ConvBase
+from bioconvert.core.decorators import requires
+
+_log = colorlog.getLogger(__name__)
+
+__all__ = ["BAM2COV"]
+
+
+class BAM2COV(ConvBase):
+    """Convert sorted :term:`BAM` file into :term:`COV` file
+
+
+    Note that the COV format is of the form::
+
+        chr1    1   0
+        chr1    2   0
+        chr1    3   0
+        chr1    4   0
+        chr1    5   0
+
+    that is contig name, position, coverage.
+
+    .. warning:: the BAM file must be sorted. This can be achieved with
+        bamtools using *bamtools sort -in INPUT.bam*
+
+    Methods available are based on samtools [SAMTOOLS]_ or bedtools [BEDTOOLS]_.
+    """
+
+    #: Default value
+    # _default_method = "samtools"
+    _default_method = "bedtools"
+
+    def __init__(self, infile, outfile):
+        """.. rubric:: Constructor
+
+        :param str infile: The path to the input BAM file. **It must be sorted**.
+        :param str outfile: The path to the output file
+        """
+        super().__init__(infile, outfile)
+
+    @requires("samtools")
+    def _method_samtools(self, *args, **kwargs):
+        """Do the conversion sorted :term:`BAM` -> :term:`BED` using samtools
+
+        `SAMtools documentation <http://www.htslib.org/doc/samtools.html>`_"""
+        cmd = "samtools depth -aa {} > {}".format(self.infile, self.outfile)
+        self.execute(cmd)
+
+    @requires("bedtools")
+    def _method_bedtools(self, *args, **kwargs):
+        """Do the conversion sorted :term:`BAM` -> :term:`BED` using bedtools
+
+        `bedtools documentation <https://bedtools.readthedocs.io/en/latest/>`_"""
+        cmd = "bedtools genomecov -d -ibam {} > {}".format(self.infile, self.outfile)
+        self.execute(cmd)

bioconvert/bam2cram.py

@@ -0,0 +1,90 @@
+###########################################################################
+# Bioconvert is a project to facilitate the interconversion               #
+# of life science data from one format to another.                        #
+#                                                                         #
+# Copyright © 2018-2022  Institut Pasteur, Paris and CNRS.                #
+#                                                                         #
+# bioconvert is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by    #
+# the Free Software Foundation, either version 3 of the License, or       #
+# (at your option) any later version.                                     #
+#                                                                         #
+# bioconvert is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
+# GNU General Public License for more details.                            #
+#                                                                         #
+# You should have received a copy of the GNU General Public License       #
+# along with this program (COPYING file).                                 #
+# If not, see <http://www.gnu.org/licenses/>.                             #
+#                                                                         #
+# Repository: https://github.com/bioconvert/bioconvert                    #
+# Documentation: http://bioconvert.readthedocs.io                         #
+###########################################################################
+"""Convert :term:`BAM` file to :term:`CRAM` format"""
+import os
+
+import colorlog
+
+from bioconvert import ConvBase
+from bioconvert.core.base import ConvArg
+from bioconvert.core.decorators import requires
+
+logger = colorlog.getLogger(__name__)
+
+
+class BAM2CRAM(ConvBase):
+    """Convert :term:`BAM` file to :term:`CRAM` file
+
+    The conversion requires the reference corresponding to the input file
+    It can be provided as an argument with the standalone (*-\\-reference*).
+    Otherwise, users are asked to provide it.
+
+    Methods available are based on samtools [SAMTOOLS]_.
+    """
+
+    #: Default value
+    _default_method = "samtools"
+    _threading = True
+
+    def __init__(self, infile, outfile, *args, **kargs):
+        """.. rubric:: constructor
+
+        :param str infile: input BAM file
+        :param str outfile: output CRAM filename
+
+        """
+        super(BAM2CRAM, self).__init__(infile, outfile, *args, **kargs)
+
+    def _get_reference(self):
+        # In case the --reference is not used
+        msg = "Please enter the reference corresponding "
+        msg += "to the input BAM file:"
+        reference = input(msg)
+        if os.path.exists(reference) is False:
+            raise IOError("Reference required")
+        else:
+            logger.debug("Reference exists ({}).".format(reference))
+        return reference
+
+    @requires("samtools")
+    def _method_samtools(self, *args, **kwargs):
+        """Here we use the SAMtools tool.
+
+        `SAMtools documentation <http://www.htslib.org/doc/samtools.html>`_"""
+        # -C means output is CRAM
+
+        reference = kwargs.get("reference", None)
+        if reference is None:
+            reference = self._get_reference()
+
+        cmd = "samtools view -@ {} -C {} -T {} -o {}".format(self.threads, self.infile, reference, self.outfile)
+        self.execute(cmd)
+
+    @classmethod
+    def get_additional_arguments(cls):
+        yield ConvArg(
+            names="--reference",
+            default=None,
+            help="the reference used (FASTA format). If not provided, prompt will appear",
+        )