def get_viewer_html(id_res):
"""
Get HTML file with offline interactive viewer inside
:param id_res: job id
:type id_res: str
"""
paf = 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, idx1, idx2)
if paf.parsed:
res = paf.get_d3js_data()
res["success"] = True
percents = paf.get_summary_stats()
with open(
os.path.join(app_folder, "static", "js",
"dgenies-offline-result.min.js"), "r") as js_min:
js = js_min.read()
with open(
os.path.join(app_folder, "static", "css",
"dgenies-offline-result.min.css"),
"r") as css_min:
css = css_min.read()
return render_template("map_offline.html",
json=json.dumps(res),
version=VERSION,
js=js,
css=css,
percents=percents)
return abort(403)
def summary(id_res):
"""
Get Dot plot summary data
: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")
try:
paf = Paf(paf_file, idx1, idx2, False)
except FileNotFoundError:
return jsonify({"success": False, "message": "Unable to load data!"})
percents = None
s_status = "waiting" # Accepted values: waiting, done, fail
status_file = os.path.join(APP_DATA, id_res, ".summarize")
fail_file = status_file + ".fail"
if not os.path.exists(status_file): # The job is finished or not started
if not os.path.exists(
fail_file
): # The job has not started yet or has successfully ended
percents = paf.get_summary_stats()
if percents is None: # The job has not started yet
Path(status_file).touch()
thread = threading.Timer(0,
paf.build_summary_stats,
kwargs={"status_file": status_file})
thread.start()
else: # The job has successfully ended
s_status = "done"
else: # The job has failed
s_status = "fail"
if s_status == "waiting": # The job is running
# Check if the job end in the next 30 seconds
nb_iter = 0
while os.path.exists(status_file) and not os.path.exists(
fail_file) and nb_iter < 10:
time.sleep(3)
nb_iter += 1
if not os.path.exists(status_file): # The job has ended
percents = paf.get_summary_stats()
if percents is None: # The job has failed
s_status = "fail"
else: # The job has successfully ended
s_status = "done"
if s_status == "fail":
return jsonify({
"success":
False,
"message":
"Build of summary failed. Please contact us to report the bug"
})
return jsonify({"success": True, "percents": percents, "status": s_status})
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 get_graph():
"""
Get dot plot data for a job
"""
id_f = request.form["id"]
paf = os.path.join(APP_DATA, id_f, "map.paf")
idx1 = os.path.join(APP_DATA, id_f, "query.idx")
idx2 = os.path.join(APP_DATA, id_f, "target.idx")
paf = Paf(paf, idx1, idx2)
if paf.parsed:
valid = os.path.join(APP_DATA, id_f, ".valid")
if not os.path.exists(valid):
Path(valid).touch()
res = paf.get_d3js_data()
res["success"] = True
return jsonify(res)
return jsonify({"success": False, "message": paf.error})
def no_assoc(id_res):
"""
Get contigs that match with None target
:param id_res: job id
:type id_res: str
"""
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)
except FileNotFoundError:
print("Unable to load data!")
abort(404)
return False
file_content = paf.build_list_no_assoc(request.form["to"])
empty = file_content == "\n"
return jsonify({"file_content": file_content, "empty": empty})
abort(404)
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)
def sort_graph(id_res):
"""
Sort dot plot to referene
:param id_res: job id
:type id_res: str
"""
if not os.path.exists(os.path.join(APP_DATA, id_res, ".all-vs-all")):
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.sort()
if paf.parsed:
res = paf.get_d3js_data()
res["success"] = True
return jsonify(res)
return jsonify({"success": False, "message": paf.error})
return jsonify({
"success": False,
"message": "Sort is not available for All-vs-All mode"
})
def reverse_contig(id_res):
"""
Reverse contig order
:param id_res: job id
:type id_res: str
"""
contig_name = request.form["contig"]
if not os.path.exists(os.path.join(APP_DATA, id_res, ".all-vs-all")):
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.reverse_contig(contig_name)
if paf.parsed:
res = paf.get_d3js_data()
res["success"] = True
return jsonify(res)
return jsonify({"success": False, "message": paf.error})
return jsonify({
"success": False,
"message": "Sort is not available for All-vs-All mode"
})
plotdots = snakemake.params["pixels"]
paths = []
idxs = []
for i in (snakemake.input["query"], snakemake.input["reference"]):
dir = os.path.dirname(i)
file = os.path.basename(i)
print(f'Indexing {dir}/{file}...')
(success, numctgs, err) = index_file(dir, file, file + ".idx")
if not success:
print(err)
sys.exit(-1)
else:
paths.append(dir)
idxs.append(file)
# Load data structures
paf_file = snakemake.input["paf"]
idx1 = os.path.join(paths[0], idxs[0])
idx2 = os.path.join(paths[1], idxs[1])
paf = Paf(paf_file, idx1, idx2, False)
paf.sort()
# Calculate values for matrix
asize1 = map(sum, Index.load(idx1)[2])
asize2 = map(sum, Index.load(idx2)[2])
awinsize1 = asize1 / plotdots
awinsize2 = asize2 / plotdots