def build_query_as_reference(id_res):
"""
Build fasta of query with contigs order like reference
:param id_res: job id
:type id_res: str
"""
paf_file = os.path.join(APP_DATA, id_res, "map.paf")
idx1 = os.path.join(APP_DATA, id_res, "query.idx")
idx2 = os.path.join(APP_DATA, id_res, "target.idx")
paf = Paf(paf_file, idx1, idx2, False, mailer=mailer, id_job=id_res)
paf.parse_paf(False, True)
if MODE == "webserver":
thread = threading.Timer(0, paf.build_query_chr_as_reference)
thread.start()
return True
return paf.build_query_chr_as_reference()
def free_noise(id_res):
"""
Remove noise from the dot plot
:param id_res: job id
:type id_res: str
"""
paf_file = os.path.join(APP_DATA, id_res, "map.paf")
idx1 = os.path.join(APP_DATA, id_res, "query.idx")
idx2 = os.path.join(APP_DATA, id_res, "target.idx")
paf = Paf(paf_file, idx1, idx2, False)
paf.parse_paf(noise=request.form["noise"] == "1")
if paf.parsed:
res = paf.get_d3js_data()
res["success"] = True
return jsonify(res)
return jsonify({"success": False, "message": paf.error})
def qt_assoc(id_res):
"""
Query - Target association TSV file
:param id_res:
:return:
"""
res_dir = os.path.join(APP_DATA, id_res)
if os.path.exists(res_dir) and os.path.isdir(res_dir):
paf_file = os.path.join(APP_DATA, id_res, "map.paf")
idx1 = os.path.join(APP_DATA, id_res, "query.idx")
idx2 = os.path.join(APP_DATA, id_res, "target.idx")
try:
paf = Paf(paf_file, idx1, idx2, False)
paf.parse_paf(False)
except FileNotFoundError:
print("Unable to load data!")
abort(404)
return False
csv_content = paf.build_query_on_target_association_file()
return Response(csv_content, mimetype="text/plain")
abort(404)