# Copyright 2018 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Print an ASCII art pileup image."""

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

from absl import app

from nucleus.io import sam
from nucleus.util import ranges

ANSI_BOLD = '\033[1m'
ANSI_RED = '\033[91m'
ANSI_OFF = '\033[0m'

# TODO(thomaswc): Also have this print out the reference sequence at the
# top if a reference fasta file is supplied.


def read_str(left_pos, start, highlight_position, seq):
  """Returns an aligned and highlighted ASCII representation of sequence."""
  s = ' ' * (start - left_pos)
  i = highlight_position - start
  j = i + 1
  s += seq[:i] + ANSI_BOLD + ANSI_RED + seq[i:j] + ANSI_OFF + seq[j:]
  return s


def ascii_pileup(sam_filename, query):
  """Returns an ASCII pileup image for the query as a list of strings.

  Args:
    sam_filename: The filename of the BAM/SAM file.
    query: String version of range.
  """
  r = ranges.parse_literal(query)
  position = r.start

  with sam.SamReader(sam_filename) as sam_reader:
    reads = sam_reader.query(r)
    pos_seq_pairs = sorted(
        (read.alignment.position.position, read.aligned_sequence)
        for read in reads)
    if not pos_seq_pairs:
      print('No overlapping reads found for', query)
      return []

    left_position = pos_seq_pairs[0][0]
    return [read_str(left_position, start, position, seq)
            for start, seq in pos_seq_pairs]


def main(argv):
  if len(argv) != 3:
    print('Usage: {} <input_sam> <chromosome>:<position>'.format(argv[0]))
    return -1
  in_sam = argv[1]
  query = argv[2]
  print('\n'.join(ascii_pileup(in_sam, query)))


if __name__ == '__main__':
  app.run(main)

# Copyright 2018 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Print an ASCII art pileup image."""

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

from absl import app

from nucleus.io import sam
from nucleus.util import ranges

ANSI_BOLD = '\033[1m'
ANSI_RED = '\033[91m'
ANSI_OFF = '\033[0m'

# TODO(thomaswc): Also have this print out the reference sequence at the
# top if a reference fasta file is supplied.


def read_str(left_pos, start, highlight_position, seq):
  """Returns an aligned and highlighted ASCII representation of sequence."""
  s = ' ' * (start - left_pos)
  i = highlight_position - start
  j = i + 1
  s += seq[:i] + ANSI_BOLD + ANSI_RED + seq[i:j] + ANSI_OFF + seq[j:]
  return s


def ascii_pileup(sam_filename, query):
  """Returns an ASCII pileup image for the query as a list of strings.

  Args:
    sam_filename: The filename of the BAM/SAM file.
    query: String version of range.
  """
  r = ranges.parse_literal(query)
  position = r.start

  with sam.SamReader(sam_filename) as sam_reader:
    reads = sam_reader.query(r)
    pos_seq_pairs = sorted(
        (read.alignment.position.position, read.aligned_sequence)
        for read in reads)
    if not pos_seq_pairs:
      print('No overlapping reads found for', query)
      return []

    left_position = pos_seq_pairs[0][0]
    return [read_str(left_position, start, position, seq)
            for start, seq in pos_seq_pairs]


def main(argv):
  if len(argv) != 3:
    print('Usage: {} <input_sam> <chromosome>:<position>'.format(argv[0]))
    return -1
  in_sam = argv[1]
  query = argv[2]
  print('\n'.join(ascii_pileup(in_sam, query)))


if __name__ == '__main__':
  app.run(main)

# Copyright 2018 Google LLC. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # #     http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. Print an ASCII art pileup image. # TODO(thomaswc): Also have this print out the reference sequence at the # top if a reference fasta file is supplied. Returns an aligned and highlighted ASCII representation of sequence. Returns an ASCII pileup image for the query as a list of strings.    Args:     sam_filename: The filename of the BAM/SAM file.     query: String version of range.