def test_alignment_info_from_bam(self):
datum, unrolled, max_subread, movie_names = alignment_info_from_bam(
self.BAM_PATH)[self.MOVIE].as_tuple()
self.assertEqual(max_subread[(self.MOVIE, 17417)],
((self.MOVIE, 17417, 1196, 3131), 1925))
self.assertEqual(max_subread[(self.MOVIE, 27338)],
((self.MOVIE, 27338, 4356, 5498), 1115))
def _harvest_file_data(file_name):
log.info("reading {f}.pbi".format(f=file_name))
try:
return alignment_info_from_bam(file_name)
except Exception as err:
# multiprocessing does not handle uncaught Exceptions gracefully
return err
def _harvest_file_data(file_name):
log.info("reading {f}.pbi".format(f=file_name))
try:
return alignment_info_from_bam(file_name)
except Exception as err:
# multiprocessing does not handle uncaught Exceptions gracefully
return err
def test_alignment_info_from_bam(self):
datum, unrolled, max_subread, movie_names = alignment_info_from_bam(
self.BAM_PATH)[self.MOVIE].as_tuple()
self.assertEqual(max_subread[(self.MOVIE, 17417)],
((self.MOVIE, 17417, 1196, 3131), 1925))
self.assertEqual(max_subread[(self.MOVIE, 27338)],
((self.MOVIE, 27338, 4356, 5498), 1115))
def setUpClass(cls):
log.info("Loading alignments from {c}".format(c=cls.BAM_PATH))
movie_names, unrolled, datum, columns = from_alignment_file(
alignment_info_from_bam(cls.BAM_PATH)[cls.MOVIE])
cls.datum = datum
cls.unrolled = unrolled
cls.movie_names = movie_names
cls.columns = columns
def setUpClass(cls):
log.info("Loading alignments from {c}".format(c=cls.BAM_PATH))
movie_names, unrolled, datum, columns = from_alignment_file(
alignment_info_from_bam(cls.BAM_PATH)[cls.MOVIE])
cls.datum = datum
cls.unrolled = unrolled
cls.movie_names = movie_names
cls.columns = columns
def analyze_movies(movies, alignment_file_names, stats_models):
all_results = []
log.info("collecting data from {n} BAM files...".format(
n=len(alignment_file_names)))
for file_name in alignment_file_names:
log.info("reading {f}.pbi".format(f=file_name))
results = alignment_info_from_bam(file_name)
for movie, aln_info in results.iteritems():
log.info("Analyzing Movie {n} in {f}".format(n=movie, f=file_name))
args = from_alignment_file(aln_info)
_process_movie_data(movie, file_name, stats_models, *args)
log.info("Completed analyzing {n} movies.".format(n=len(movies)))
def analyze_movies(movies, alignment_file_names, stats_models):
all_results = []
log.info("collecting data from {n} BAM files...".format(
n=len(alignment_file_names)))
for file_name in alignment_file_names:
log.info("reading {f}.pbi".format(f=file_name))
results = alignment_info_from_bam(file_name)
for movie, aln_info in results.iteritems():
log.info("Analyzing Movie {n} in {f}".format(n=movie, f=file_name))
args = from_alignment_file(aln_info)
_process_movie_data(movie, file_name, stats_models, *args)
log.info("Completed analyzing {n} movies.".format(n=len(movies)))
