def _get_reads_info(aligned_reads_file):
"""
Extract information from the BAM files. Returns a tuple of length 2.
First item is a dictionary of dictionaries, such that holes are mapped by cell, then set.
Second item is the instrument name.
:param aligned_reads_file: (str) path to aligned_reads[.xml,.bam]
:return tuple (reads_by_cell_then_set, instrument) (dict, string): A dictionary of dictionaries,
instrument name
"""
inst = None
reads_by_cell = defaultdict(set)
with AlignmentSet(aligned_reads_file) as ds:
for bamfile in ds.resourceReaders():
if ds.isIndexed:
logging.info("Indexed file - will use fast loop.")
for (hole, rgId) in zip(bamfile.holeNumber, bamfile.qId):
movie_name = bamfile.readGroupInfo(rgId).MovieName
cell = movie_to_cell(movie_name)
if inst is None:
inst = _cell_2_inst(cell)
reads_by_cell[cell].add(hole)
else:
for aln in bamfile:
hole = aln.HoleNumber
movie_name = aln.movieName
cell = movie_to_cell(movie_name)
if inst is None:
inst = _cell_2_inst(cell)
reads_by_cell[cell].add(hole)
return reads_by_cell, inst
def _get_reads_info(aligned_reads_file):
"""
Extract information from the BAM files. Returns a tuple of length 2.
First item is a dictionary of dictionaries, such that holes are mapped by cell, then set.
Second item is the instrument name.
:param aligned_reads_file: (str) path to aligned_reads[.xml,.bam]
:return tuple (reads_by_cell_then_set, instrument) (dict, string): A dictionary of dictionaries,
instrument name
"""
inst = None
reads_by_cell = defaultdict(set)
with AlignmentSet(aligned_reads_file) as ds:
for bamfile in ds.resourceReaders():
if ds.isIndexed:
logging.info("Indexed file - will use fast loop.")
for (hole, rgId) in zip(bamfile.holeNumber, bamfile.qId):
movie_name = bamfile.readGroupInfo(rgId).MovieName
cell = movie_to_cell(movie_name)
if inst is None:
inst = _cell_2_inst(cell)
reads_by_cell[cell].add(hole)
else:
for aln in bamfile:
hole = aln.HoleNumber
movie_name = aln.movieName
cell = movie_to_cell(movie_name)
if inst is None:
inst = _cell_2_inst(cell)
reads_by_cell[cell].add(hole)
return reads_by_cell, inst
def test_timestamped_moviename(self):
moviename = "m54004_151002_00100"
cellname = movie_to_cell(moviename)
# XXX for the time being the cellname will be the timestamped
# moviename...
self.assertEqual(moviename, cellname)
self.assertEqual('54004', _cell_2_inst(cellname))
def test_timestamped_moviename(self):
moviename = "m54004_151002_00100"
cellname = movie_to_cell(moviename)
# XXX for the time being the cellname will be the timestamped
# moviename...
self.assertEqual(moviename, cellname)
self.assertEqual('54004', _cell_2_inst(cellname))
def test_movie_2_cell(self):
"""
Parse a cell name from a movie name
"""
try:
log.info(TestUtil.test_movie_2_cell.__doc__)
self.assertEqual('m120128_025832_42129_c100277632550000001523007907041250',
movie_to_cell('m120128_025832_42129_c100277632550000001523007907041250_s2_p0'))
except:
log.error(traceback.format_exc())
raise
def test_movie_2_cell(self):
"""
Parse a cell name from a movie name
"""
try:
log.info(TestUtil.test_movie_2_cell.__doc__)
self.assertEqual(
'm120128_025832_42129_c100277632550000001523007907041250',
movie_to_cell(
'm120128_025832_42129_c100277632550000001523007907041250_s2_p0'
))
except:
log.error(traceback.format_exc())
raise
def run(dataset_file):
"""Reads in the input.fofn and counts movies and cells. Outputs in XML."""
with openDataSet(dataset_file) as ds:
movies = None
movies = set([])
for file_name in ds.toExternalFiles():
if type(ds).__name__ == "HdfSubreadSet":
movies.add(path_to_movie(file_name))
else:
with BamReader(file_name) as bam:
for rg in bam.peer.header["RG"]:
movies.add(rg["PU"])
cells = set([movie_to_cell(movie) for movie in movies])
ncells_attr = Attribute(Constants.A_NCELLS, len(cells))
nmovies_attr = Attribute(Constants.A_NMOVIES, len(movies))
attrs = [ncells_attr, nmovies_attr]
report = Report(meta_rpt.id, attributes=attrs)
return meta_rpt.apply_view(report)
def run(dataset_file):
"""Reads in the input.fofn and counts movies and cells. Outputs in XML."""
with openDataSet(dataset_file) as ds:
movies = None
movies = set([])
for file_name in ds.toExternalFiles():
if type(ds).__name__ == "HdfSubreadSet":
movies.add( path_to_movie(file_name) )
else:
with BamReader(file_name) as bam:
for rg in bam.peer.header["RG"]:
movies.add(rg["PU"])
cells = set([ movie_to_cell(movie) for movie in movies ])
ncells_attr = Attribute('ncells', len(cells), name="SMRT Cells")
nmovies_attr = Attribute('nmovies', len(movies), name="Movies")
attrs = [ncells_attr, nmovies_attr]
report = Report('overview', attributes=attrs)
return report
def run(dataset_file):
"""Reads in the input.fofn and counts movies and cells. Outputs in XML."""
with openDataSet(dataset_file) as ds:
movies = None
movies = set([])
for file_name in ds.toExternalFiles():
if type(ds).__name__ == "HdfSubreadSet":
movies.add(path_to_movie(file_name))
else:
with BamReader(file_name) as bam:
for rg in bam.peer.header["RG"]:
movies.add(rg["PU"])
cells = set([movie_to_cell(movie) for movie in movies])
ncells_attr = Attribute(Constants.A_NCELLS, len(cells))
nmovies_attr = Attribute(Constants.A_NMOVIES, len(movies))
attrs = [ncells_attr, nmovies_attr]
report = Report(Constants.R_ID, attributes=attrs)
return spec.apply_view(report)
