def run(self):
super(JobTrestle, self).run()
if not os.path.isdir(self.work_dir):
os.mkdir(self.work_dir)
summary_file = os.path.join(self.work_dir, "trestle_summary.txt")
resolved_repeats_seqs = os.path.join(self.work_dir,
"resolved_copies.fasta")
repeat_graph = RepeatGraph(fp.read_sequence_dict(self.graph_edges))
repeat_graph.load_from_file(self.repeat_graph)
try:
repeats_info = tres_graph \
.get_simple_repeats(repeat_graph, self.reads_alignment_file,
fp.read_sequence_dict(self.graph_edges))
tres_graph.dump_repeats(
repeats_info, os.path.join(self.work_dir, "repeats_dump"))
tres.resolve_repeats(self.args, self.work_dir, repeats_info,
summary_file, resolved_repeats_seqs)
tres_graph.apply_changes(
repeat_graph, summary_file,
fp.read_sequence_dict(resolved_repeats_seqs))
except KeyboardInterrupt as e:
raise
#except Exception as e:
# logger.warning("Caught unhandled exception: " + str(e))
# logger.warning("Continuing to the next pipeline stage. "
# "Please submit a bug report along with the full log file")
repeat_graph.dump_to_file(self.out_files["repeat_graph"])
fp.write_fasta_dict(repeat_graph.edges_fasta,
self.out_files["repeat_graph_edges"])
def run(self):
super(JobShortPlasmidsAssembly, self).run()
logger.info("Recovering short unassembled sequences")
if not os.path.isdir(self.work_dir):
os.mkdir(self.work_dir)
plasmids = plas.assemble_short_plasmids(self.args, self.work_dir,
self.contigs_path)
#updating repeat graph
repeat_graph = RepeatGraph(fp.read_sequence_dict(self.graph_edges))
repeat_graph.load_from_file(self.repeat_graph)
plas.update_graph(repeat_graph, plasmids)
repeat_graph.dump_to_file(self.out_files["repeat_graph"])
fp.write_fasta_dict(repeat_graph.edges_fasta,
self.out_files["repeat_graph_edges"])