# Copyright 2018 Google Inc.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
#    contributors may be used to endorse or promote products derived from this
#    software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Classes for reading and writing BedGraph files.

The BedGraph format is described at
https://genome.ucsc.edu/goldenpath/help/bedgraph.html

API for reading:

```python
from third_party.nucleus.io import bedgraph

# Iterate through all records.
with bed.BedGraphReader(input_path) as reader:
  for record in reader:
    print(record)
```

where `record` is a `nucleus.genomics.v1.BedGraphRecord` protocol buffer.

API for writing:

```python
from third_party.nucleus.io import bedgraph
from third_party.nucleus.protos import bedgraph_pb2

# records is an iterable of nucleus.genomics.v1.BedGraphRecord protocol buffers.
records = ...

# Write all records to the desired output path.
with bed.BedGraphWriter(output_path) as writer:
  for record in records:
    writer.write(record)
```

For both reading and writing, if the path provided to the constructor contains
'.tfrecord' as an extension, a `TFRecord` file is assumed and attempted to be
read or written. Otherwise, the filename is treated as a true BedGraph file.

Files that end in a '.gz' suffix cause the file to be treated as compressed
(with BGZF if it is a BedGraph file, and with gzip if it is a TFRecord file).
"""

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

from third_party.nucleus.io import genomics_reader
from third_party.nucleus.io import genomics_writer
from third_party.nucleus.io.python import bedgraph_reader
from third_party.nucleus.io.python import bedgraph_writer
from third_party.nucleus.protos import bedgraph_pb2


class NativeBedGraphReader(genomics_reader.GenomicsReader):
  """Class for reading from native BedGraph files.

  Most users will want to use BedGraphReader instead, because it dynamically
  dispatches between reading native BedGraph files and TFRecord files based on
  the filename's extension.
  """

  def __init__(self, input_path, num_fields=0):
    """Initializes a NativeBedGraphReader.

    Args:
      input_path: string. A path to a resource containing BedGraph records.
      num_fields: int. The number of fields to read in the BedGraph. If unset or
        set to zero, all fields in the input are read.
    """
    super(NativeBedGraphReader, self).__init__()

    bedgraph_path = input_path.encode('utf8')
    self._reader = bedgraph_reader.BedGraphReader.from_file(bedgraph_path)

  def query(self):
    """Returns an iterator for going through the records in the region.

    NOTE: This function is not currently implemented by NativeBedGraphReader
    though it could be implemented for sorted, tabix-indexed BedGraph files.
    """
    raise NotImplementedError('Can not currently query a BedGraph file')

  def iterate(self):
    """Returns an iterable of BedGraphRecord protos in the file."""
    return self._reader.iterate()

  def __exit__(self, exit_type, exit_value, exit_traceback):
    self._reader.__exit__(exit_type, exit_value, exit_traceback)


class BedGraphReader(genomics_reader.DispatchingGenomicsReader):
  """Class for reading BedGraphRecord protos from BedGraph or TFRecord files."""

  def _native_reader(self, input_path, **kwargs):
    return NativeBedGraphReader(input_path, **kwargs)

  def _record_proto(self):
    return bedgraph_pb2.BedGraphRecord


class NativeBedGraphWriter(genomics_writer.GenomicsWriter):
  """Class for writing to native BedGraph files.

  Most users will want BedGraphWriter, which will write to either native
  BedGraph files or TFRecord files, based on the output filename's extension.
  """

  def __init__(self, output_path, header=None):
    """Initializer for NativeBedGraphWriter.

    Args:
      output_path: str. The path to which to write the BedGraph file.
    """
    super(NativeBedGraphWriter, self).__init__()
    self._writer = bedgraph_writer.BedGraphWriter.to_file(output_path)

  def write(self, proto):
    self._writer.write(proto)

  def __exit__(self, exit_type, exit_value, exit_traceback):
    self._writer.__exit__(exit_type, exit_value, exit_traceback)


class BedGraphWriter(genomics_writer.DispatchingGenomicsWriter):
  """Class for writing BedGraphRecord protos to BedGraph or TFRecord files."""

  def _native_writer(self, output_path):
    return NativeBedGraphWriter(output_path)

# Copyright 2018 Google Inc.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
#    this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
#    notice, this list of conditions and the following disclaimer in the
#    documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
#    contributors may be used to endorse or promote products derived from this
#    software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""Classes for reading and writing BedGraph files.

The BedGraph format is described at
https://genome.ucsc.edu/goldenpath/help/bedgraph.html

API for reading:

```python
from third_party.nucleus.io import bedgraph

# Iterate through all records.
with bed.BedGraphReader(input_path) as reader:
  for record in reader:
    print(record)
```

where `record` is a `nucleus.genomics.v1.BedGraphRecord` protocol buffer.

API for writing:

```python
from third_party.nucleus.io import bedgraph
from third_party.nucleus.protos import bedgraph_pb2

# records is an iterable of nucleus.genomics.v1.BedGraphRecord protocol buffers.
records = ...

# Write all records to the desired output path.
with bed.BedGraphWriter(output_path) as writer:
  for record in records:
    writer.write(record)
```

For both reading and writing, if the path provided to the constructor contains
'.tfrecord' as an extension, a `TFRecord` file is assumed and attempted to be
read or written. Otherwise, the filename is treated as a true BedGraph file.

Files that end in a '.gz' suffix cause the file to be treated as compressed
(with BGZF if it is a BedGraph file, and with gzip if it is a TFRecord file).
"""

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

from third_party.nucleus.io import genomics_reader
from third_party.nucleus.io import genomics_writer
from third_party.nucleus.io.python import bedgraph_reader
from third_party.nucleus.io.python import bedgraph_writer
from third_party.nucleus.protos import bedgraph_pb2


class NativeBedGraphReader(genomics_reader.GenomicsReader):
  """Class for reading from native BedGraph files.

  Most users will want to use BedGraphReader instead, because it dynamically
  dispatches between reading native BedGraph files and TFRecord files based on
  the filename's extension.
  """

  def __init__(self, input_path, num_fields=0):
    """Initializes a NativeBedGraphReader.

    Args:
      input_path: string. A path to a resource containing BedGraph records.
      num_fields: int. The number of fields to read in the BedGraph. If unset or
        set to zero, all fields in the input are read.
    """
    super(NativeBedGraphReader, self).__init__()

    bedgraph_path = input_path.encode('utf8')
    self._reader = bedgraph_reader.BedGraphReader.from_file(bedgraph_path)

  def query(self):
    """Returns an iterator for going through the records in the region.

    NOTE: This function is not currently implemented by NativeBedGraphReader
    though it could be implemented for sorted, tabix-indexed BedGraph files.
    """
    raise NotImplementedError('Can not currently query a BedGraph file')

  def iterate(self):
    """Returns an iterable of BedGraphRecord protos in the file."""
    return self._reader.iterate()

  def __exit__(self, exit_type, exit_value, exit_traceback):
    self._reader.__exit__(exit_type, exit_value, exit_traceback)


class BedGraphReader(genomics_reader.DispatchingGenomicsReader):
  """Class for reading BedGraphRecord protos from BedGraph or TFRecord files."""

  def _native_reader(self, input_path, **kwargs):
    return NativeBedGraphReader(input_path, **kwargs)

  def _record_proto(self):
    return bedgraph_pb2.BedGraphRecord


class NativeBedGraphWriter(genomics_writer.GenomicsWriter):
  """Class for writing to native BedGraph files.

  Most users will want BedGraphWriter, which will write to either native
  BedGraph files or TFRecord files, based on the output filename's extension.
  """

  def __init__(self, output_path, header=None):
    """Initializer for NativeBedGraphWriter.

    Args:
      output_path: str. The path to which to write the BedGraph file.
    """
    super(NativeBedGraphWriter, self).__init__()
    self._writer = bedgraph_writer.BedGraphWriter.to_file(output_path)

  def write(self, proto):
    self._writer.write(proto)

  def __exit__(self, exit_type, exit_value, exit_traceback):
    self._writer.__exit__(exit_type, exit_value, exit_traceback)


class BedGraphWriter(genomics_writer.DispatchingGenomicsWriter):
  """Class for writing BedGraphRecord protos to BedGraph or TFRecord files."""

  def _native_writer(self, output_path):
    return NativeBedGraphWriter(output_path)

# Copyright 2018 Google Inc. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions # are met: # # 1. Redistributions of source code must retain the above copyright notice, #    this list of conditions and the following disclaimer. # # 2. Redistributions in binary form must reproduce the above copyright #    notice, this list of conditions and the following disclaimer in the #    documentation and/or other materials provided with the distribution. # # 3. Neither the name of the copyright holder nor the names of its #    contributors may be used to endorse or promote products derived from this #    software without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. Classes for reading and writing BedGraph files.  The BedGraph format is described at https://genome.ucsc.edu/goldenpath/help/bedgraph.html  API for reading:  ```python from third_party.nucleus.io import bedgraph  # Iterate through all records. with bed.BedGraphReader(input_path) as reader:   for record in reader:     print(record) ```  where `record` is a `nucleus.genomics.v1.BedGraphRecord` protocol buffer.  API for writing:  ```python from third_party.nucleus.io import bedgraph from third_party.nucleus.protos import bedgraph_pb2  # records is an iterable of nucleus.genomics.v1.BedGraphRecord protocol buffers. records = ...  # Write all records to the desired output path. with bed.BedGraphWriter(output_path) as writer:   for record in records:     writer.write(record) ```  For both reading and writing, if the path provided to the constructor contains '.tfrecord' as an extension, a `TFRecord` file is assumed and attempted to be read or written. Otherwise, the filename is treated as a true BedGraph file.  Files that end in a '.gz' suffix cause the file to be treated as compressed (with BGZF if it is a BedGraph file, and with gzip if it is a TFRecord file). Class for reading from native BedGraph files.    Most users will want to use BedGraphReader instead, because it dynamically   dispatches between reading native BedGraph files and TFRecord files based on   the filename's extension. Initializes a NativeBedGraphReader.      Args:       input_path: string. A path to a resource containing BedGraph records.       num_fields: int. The number of fields to read in the BedGraph. If unset or         set to zero, all fields in the input are read. Returns an iterator for going through the records in the region.      NOTE: This function is not currently implemented by NativeBedGraphReader     though it could be implemented for sorted, tabix-indexed BedGraph files. Returns an iterable of BedGraphRecord protos in the file. Class for reading BedGraphRecord protos from BedGraph or TFRecord files. Class for writing to native BedGraph files.    Most users will want BedGraphWriter, which will write to either native   BedGraph files or TFRecord files, based on the output filename's extension. Initializer for NativeBedGraphWriter.      Args:       output_path: str. The path to which to write the BedGraph file. Class for writing BedGraphRecord protos to BedGraph or TFRecord files.