def to_summary(self, filename="sequana_summary_pacbio_ccs.json"):
"""Save statistics into a JSON file
:param filename:
:param data: dictionary to save. If not provided, use :meth:`stats`
"""
data = self.stats()
s = Summary("pacbio_ccs", self.sample_name, data=data)
s._data_description = {
"N": "CCS reads",
"total_bases": "Number of CCS bases",
"mean_read_length": "CCS Read Length (mean)",
"mean_nb_passes": "Number of Passes (mean)"
}
s.to_json(filename)
def to_summary(self, filename="sequana_summary_pacbio_ccs.json"):
"""Save statistics into a JSON file
:param filename:
:param data: dictionary to save. If not provided, use :meth:`stats`
"""
data = self.stats()
s = Summary("pacbio_ccs", self.sample_name, data=data)
s._data_description = {
"N": "CCS reads",
"total_bases": "Number of CCS bases",
"mean_read_length": "CCS Read Length (mean)",
"mean_nb_passes": "Number of Passes (mean)"
}
s.to_json(filename)
def get_stats(pattern, mode):
data = [[], []]
for filename in glob.glob(pattern + "/data/{}_sirv.sam".format(mode)):
b = isoseq.PacbioIsoSeqMappedIsoforms(filename)
N = Summary(filename.split("/")[0] +
"/sequana_summary_isoseq.json").data["hq_isoform"]['N']
data[0].append(N)
data[1].append(len(b.df.query("reference_name not in [-1, '-1']")))
print("scanned {}".format(filename))
return data
def to_summary(self, filename="sequana_summary_isoseq.json", data=None):
"""Save statistics into a JSON file
:param filename:
:param data: dictionary to save. If not provided, use :meth:`stats`
"""
from sequana.summary import Summary
if data is None:
data = self.stats()
Summary("isoseq",self.sample_name, data=data).to_json(filename)
def test_summary():
s = Summary("test2", sample_name="chr1",data={"mean":1})
assert s.data == {"mean":1}
assert s.version
assert s.date
d = s.as_dict()
assert "name" in d
assert "version" in d
assert "data" in d
assert "date" in d
# test wrong constructor
try:
s = Summary("test")
assert False
except:
assert True
try:
s = Summary("test", "test")
assert False
except:
assert True
# test data_description
s = Summary("test2", data={"mean":1})
s.data_description = {"mean": "mean of the data set"}
assert s.data_description == {"mean": "mean of the data set"}
try:
s.data_description = {"dummy": 1}
assert False
except:
assert True
from easydev import TempFile
with TempFile(suffix=".json") as fh:
s.to_json(fh.name)