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])