def _parse_repeats(self):
self.repeats = []
if "repeats"in self.config:
for d in self.config["repeats"]:
fname = os.path.join(self.base, d["path"])
tabix_fname = _create_tabix(fname, "bed")
d["path"] = fname
d["tabix"] = tabix_fname
self.repeats.append(d)
def _parse_repeats(self):
self.repeats = []
if "repeats" in self.config:
for d in self.config["repeats"]:
fname = os.path.join(self.base, d["path"])
tabix_fname = _create_tabix(fname, "bed")
d["path"] = fname
d["tabix"] = tabix_fname
self.repeats.append(d)
def _parse_annotation(self, reannotate=False):
if not self.config.has_key("annotation") or len(
self.config["annotation"]) == 0:
self.logger.error("No annotation files specified.")
sys.exit(1)
self.anno_files = []
self.chroms = {}
for d in self.config["annotation"]:
self.logger.debug("annotation: %s", d)
fname = os.path.join(self.base, d["path"])
t = d["type"].lower()
min_exons = 2
if d.has_key("min_exons"):
min_exons = d["min_exons"]
if d.has_key("keep") and d["keep"]:
self.keep.append(fname)
if d.has_key("filter") and d["filter"]:
self.filter.append(fname)
if d.has_key("experimental") and d["experimental"]:
self.experimental.append(fname)
if not t in VALID_TYPES:
self.logger.error("Invalid type: %s", t)
sys.exit(1)
if not os.path.exists(fname):
self.logger.error("File does not exist: %s", fname)
sys.exit(1)
else:
tabix_file = ""
if not reannotate:
tabix_file = _create_tabix(fname, t)
# Save chromosome names
for chrom in pysam.Tabixfile(tabix_file).contigs:
self.chroms[chrom] = 1
# Add file info
self.anno_files.append(
[d["name"], fname, tabix_file, t, min_exons])
def _parse_annotation(self, reannotate=False):
if not self.config.has_key("annotation") or len(self.config["annotation"]) == 0:
self.logger.error("No annotation files specified.")
sys.exit(1)
self.anno_files = []
self.chroms = {}
for d in self.config["annotation"]:
self.logger.debug("annotation: %s", d)
fname = os.path.join(self.base, d["path"])
t = d["type"].lower()
min_exons = 2
if d.has_key("min_exons"):
min_exons = d["min_exons"]
if d.has_key("keep") and d["keep"]:
self.keep.append(fname)
if d.has_key("filter") and d["filter"]:
self.filter.append(fname)
if d.has_key("experimental") and d["experimental"]:
self.experimental.append(fname)
if not t in VALID_TYPES:
self.logger.error("Invalid type: %s", t)
sys.exit(1)
if not os.path.exists(fname):
self.logger.error("File does not exist: %s", fname)
sys.exit(1)
else:
tabix_file = ""
if not reannotate:
tabix_file = _create_tabix(fname, t)
# Save chromosome names
for chrom in pysam.Tabixfile(tabix_file).contigs:
self.chroms[chrom] = 1
# Add file info
self.anno_files.append([d["name"], fname, tabix_file, t, min_exons])
