def test_xform_script_for_preads():
# Technically, we never have more than one daligner in a script, but that
# could change in pbsmrtpipe, since it limits the number of chunks.
script = 'daligner x y\nLAsort a b\ndaligner x1 y1\n'
expected = 'daligner_p x y\nLAsort a b\ndaligner_p x1 y1\n'
result = f.xform_script_for_preads(script)
eq_(result, expected)
script = 'daligner x y\nLAsort a b\ndaligner x1 y1\n'
expected = script # no-op
result = f.xform_script_for_raw_reads(script)
eq_(result, expected)
eq_(f.get_script_xformer(True), f.xform_script_for_preads)
eq_(f.get_script_xformer(False), f.xform_script_for_raw_reads)
def test_xform_script_for_preads():
# Technically, we never have more than one daligner in a script, but that
# could change in pbsmrtpipe, since it limits the number of chunks.
script = 'daligner x y\nLAsort a b\ndaligner x1 y1\n'
expected = 'daligner_p x y\nLAsort a b\ndaligner_p x1 y1\n'
result = f.xform_script_for_preads(script)
eq_(result, expected)
script = 'daligner x y\nLAsort a b\ndaligner x1 y1\n'
expected = script # no-op
result = f.xform_script_for_raw_reads(script)
eq_(result, expected)
eq_(f.get_script_xformer(True), f.xform_script_for_preads)
eq_(f.get_script_xformer(False), f.xform_script_for_raw_reads)
def write_run_daligner_chunks_falcon(
pread_aln,
chunk_file,
config_json_fn,
run_jobs_fn,
max_total_nchunks,
dir_name,
chunk_base_name,
chunk_ext,
chunk_keys):
db_prefix = 'preads' if pread_aln else 'raw_reads'
xform_script = get_script_xformer(pread_aln)
def chunk():
# cmds is actually a list of small bash scripts, including linefeeds.
cmds = get_daligner_job_descriptions(open(run_jobs_fn), db_prefix).values()
if max_total_nchunks < len(cmds):
log.debug("max_total_nchunks < # daligner cmds: %d < %d" %(
max_total_nchunks, len(cmds)))
cmds = joined_strs(cmds, max_total_nchunks)
symlink_dazzdb(os.path.dirname(run_jobs_fn), db_prefix)
for i, script in enumerate(cmds):
chunk_id = '_'.join([chunk_base_name, str(i)])
chunk_name = '.'.join([chunk_id, chunk_ext])
chunk_path = os.path.join(dir_name, chunk_name)
script = xform_script(script)
open(chunk_path, 'w').write(script)
d = {}
d[chunk_keys[1]] = os.path.abspath(chunk_path)
d[chunk_keys[0]] = config_json_fn
c = PipelineChunk(chunk_id, **d)
yield c
chunks = list(chunk())
write_pipeline_chunks(chunks, chunk_file, comment=None)
def write_run_daligner_chunks_falcon(pread_aln, chunk_file, config_json_fn,
run_jobs_fn, max_total_nchunks, dir_name,
chunk_base_name, chunk_ext, chunk_keys):
db_prefix = 'preads' if pread_aln else 'raw_reads'
xform_script = get_script_xformer(pread_aln)
def chunk():
# cmds is actually a list of small bash scripts, including linefeeds.
cmds = get_daligner_job_descriptions(open(run_jobs_fn),
db_prefix).values()
if max_total_nchunks < len(cmds):
log.debug("max_total_nchunks < # daligner cmds: %d < %d" %
(max_total_nchunks, len(cmds)))
cmds = joined_strs(cmds, max_total_nchunks)
symlink_dazzdb(os.path.dirname(run_jobs_fn), db_prefix)
for i, script in enumerate(cmds):
chunk_id = '_'.join([chunk_base_name, str(i)])
chunk_name = '.'.join([chunk_id, chunk_ext])
chunk_path = os.path.join(dir_name, chunk_name)
script = xform_script(script)
open(chunk_path, 'w').write(script)
d = {}
d[chunk_keys[1]] = os.path.abspath(chunk_path)
d[chunk_keys[0]] = config_json_fn
c = PipelineChunk(chunk_id, **d)
yield c
chunks = list(chunk())
write_pipeline_chunks(chunks, chunk_file, comment=None)
