def set_object(self, obj, path, plain_text=False):
from nesoni import io
temp_filename = self._object_filename('tempfile')
if plain_text:
f = open(temp_filename, 'wb')
f.write(repr(obj))
f.close()
else:
f = io.Pipe_writer(temp_filename, ['gzip'])
cPickle.dump(obj, f, 2)
f.close()
os.rename(temp_filename, self._object_filename(path))
def run(self):
workspace = working_directory.Working(self.output_dir)
workspace.setup_reference(self.reference)
workspace.update_param(snp_cost = self.snp_cost)
#assert os.path.exists(self.reference), 'Reference file does not exist'
#reference_filename = workspace._object_filename('reference.fa')
#if os.path.exists(reference_filename):
# os.unlink(reference_filename)
#os.symlink(os.path.relpath(self.reference, self.output_dir), reference_filename)
bam_filename = io.abspath(self.output_dir, 'alignments.bam')
bam_prefix = io.abspath(self.output_dir, 'alignments')
if sam.is_bam(self.input):
sort_input_filename = self.input
temp_filename = None
else:
temp_filename = io.abspath(self.output_dir, 'temp.bam')
sort_input_filename = temp_filename
writer = io.Pipe_writer(temp_filename, ['samtools', 'view', '-S', '-b', '-'])
f = open(self.input, 'rb')
while True:
data = f.read(1<<20)
if not data: break
writer.write(data)
writer.close()
f.close()
grace.status('Sort')
#io.execute([
# 'samtools', 'sort', '-n', sort_input_filename, bam_prefix
#])
sam.sort_bam(sort_input_filename, bam_prefix, by_name=True)
if temp_filename is not None:
os.unlink(temp_filename)
grace.status('')
def __init__(self, filename, headers=''):
self.writer = io.Pipe_writer(filename, ['samtools', 'view', '-S', '-b', '-'])
self.writer.write(headers)