def database():
database_form = DatabaseForm()
if database_form.validate_on_submit():
data = database_form.data
query = data["query"]
res = []
each = {}
if data["select"] == "specie":
query_data = Specie.objects(kegg_id=query)
for item in query_data:
each["kegg_id"] = item.kegg_id
each["specie_name"] = item.specie_name
res.append(each)
return render_template("home/database.html", form=database_form, res=res, type="specie")
else:
query_data = SrrTask.objects(_id__icontains=query)
for item in query_data:
each["_id"] = item._id
each["kegg_id"] = item.kegg_id
each["method"] = item.method
res.append(each)
query_data2 = SrrTask.objects(kegg_id=query)
for item in query_data2:
each["_id"] = item._id
each["kegg_id"] = item.kegg_id
each["method"] = item.method
each["browse_link"] = item.browse_link
res.append(each)
return render_template("home/database.html", form=database_form, res=res, type="srr_task")
return render_template("home/database.html", form=database_form, res=None, type=None)
def srr_task_nums(_id=None, page=None):
if page is None:
page = 1
srr_task_query = SrrTask.objects(_id=_id).first()
page_data = srr_task_query.paginate_field("srr_nums",
page=page,
per_page=50)
return render_template("admin/srr_task_nums.html", page_data=page_data)
def operon_predict(srr_list, kegg_id, soft, method, corr, srr_id):
if len(srr_list) == 1:
soft = "rockhopper"
all_srr_list = []
paired_or_not_list = []
download_path_list = []
i_iter = 0
for con in srr_list:
condition_path = os.path.join(path, srr_id, "fastq", "c" + str(i_iter))
if not os.path.exists(condition_path):
os.makedirs(condition_path)
for rep in con:
tmp_ = get_paired_or_singled(rep)
if tmp_ == 0:
soft = "rockhopper"
paired_or_not_list.append(tmp_)
all_srr_list.append(rep)
download_path_list.append(condition_path)
i_iter = i_iter + 1
pool = Pool(process)
_list = pool.starmap(srr_n_to_fastq, zip(all_srr_list, paired_or_not_list, download_path_list))
pool.close()
pool.join()
kegg_path = download_annotation(kegg_id, path)
browse_link = "http://" + "127.0.0.1" + "/JBrowse/?data=" + srr_id
if soft == "rockhopper":
condition_str = get_condition_str_rockhopper(download_path_list, paired_or_not_list, all_srr_list)
rockhopper_path = os.path.join(path, "tools", "Rockhopper.jar")
out_path = os.path.join(path, srr_id, "operon")
os.system("java -Xmx3g -cp " + rockhopper_path + " Rockhopper -p " + str(process) + " -g " + kegg_path + " " +
condition_str + " -o " + out_path)
extract_Synonym(kegg_path, out_path)
get_operon(out_path)
new_srr_task = SrrTask(_id=srr_id, kegg_id=kegg_id, operon_path="/instance/" + srr_id +
"/operon/operon.txt", method="rockhopper",
add_time=datetime.now(), bw_path="/instance/" + srr_id +
"/operon/operon.txt", browse_link=browse_link)
new_srr_task.get_srr_nums(srr_list)
new_srr_task.get_operons_from_file(os.path.join(out_path, "operon.txt"))
new_srr_task.save()
res2jbrowse(kegg_path, out_path, srr_id)
else:
input_path = os.path.join(path, "fastq")
fna_path = os.path.join(kegg_path, kegg_id + ".fna")
gff_path = os.path.join(kegg_path, kegg_id + ".gff")
out_path = os.path.join(path, srr_id, "operon")
print(input_path,fna_path,gff_path,out_path)
if corr == "c_i_j":
os.system("operondemmo -i " + input_path + " -g " + gff_path + " -f " + fna_path
+ " -m " + method + " -p " + str(process) + " -t 0.6 " + " -o " + out_path)
elif corr == "spearman":
os.system("operondemmo -i " + input_path + " -g " + gff_path + " -f " + fna_path
+ " -m " + method + " -p " + str(process) + " -t 0.6 " + " -o " + out_path + " --spearman")
else:
os.system("operondemmo -i " + input_path + " -g " + gff_path + " -f " + fna_path
+ " -m " + method + " -p " + str(process) + " -t 0.6 " + " -o " + out_path + " --person")
new_srr_task = SrrTask(_id=srr_id, kegg_id=kegg_id, operon_path="/instance/" + srr_id +
"/operon/operon.txt", method=method,
add_time=datetime.now(), bw_path="/instance/" + srr_id +
"/operon/operon.txt", browse_link=browse_link)
new_srr_task.get_srr_nums(srr_list)
new_srr_task.get_operons_from_file(os.path.join(out_path, "operon.txt"))
new_srr_task.save()
res2jbrowse(kegg_path, out_path, srr_id)
task_query = TaskId.objects.get_or_404(srr_id=srr_id)
msg = Message("OperondemmoDB Task", sender=sender, recipients=[task_query.email])
msg.body = "your task link: " + self_link + "/task/" + task_query.task_id
send_async_email(app, msg)
print("send it OK")
def srr_task_del(_id=None):
SrrTask.objects(_id=_id).delete()
flash("delete it done !", "ok")
return redirect(url_for("admin.srr_task"))
def srr_task_edit(_id=None):
srr_task_form = SrrTaskForm()
srr_task_query = SrrTask.objects.get_or_404(_id=_id)
old_bw_path = srr_task_query.bw_path
old_operon_path = srr_task_query.operon_path
if srr_task_form.validate_on_submit():
data = srr_task_form.data
SrrTask.objects(_id=_id).update_one(set__kegg_id=data["kegg_id"])
SrrTask.objects(_id=_id).update_one(
set__browse_link=data["browse_link"])
SrrTask.objects(_id=_id).update_one(set__bw_path=data["bw_path"])
SrrTask.objects(_id=_id).update_one(
set__operon_path=data["operon_path"])
SrrTask.objects(_id=_id).update_one(set__method=data["method"])
SrrTask.objects(_id=_id).update_one(set__add_time=datetime.now())
if not os.path.exists(data["bw_path"]):
os.makedirs(data["bw_path"])
os.system("mv " + old_bw_path + " " + data["bw_path"])
if not os.path.exists(data["operon_path"]):
os.makedirs(data["operon_path"])
os.system("mv " + old_operon_path + " " + data["operon_path"])
flash("edit done !", "ok")
return redirect(url_for("admin.srr_task_edit", _id=_id))
return render_template("admin/srr_task_edit.html",
form=srr_task_form,
srr_task=srr_task_query)
def srr_task_add():
srr_task_form = SrrTaskForm()
if srr_task_form.condition_add.data:
srr_task_form.condition.append_entry()
return render_template("admin/srr_task_add.html", form=srr_task_form)
i_iter = 0
for con in srr_task_form.condition.entries:
if con.condition_del.data:
srr_task_form.condition.entries.pop(i_iter)
return render_template("admin/srr_task_add.html",
form=srr_task_form)
if con.repeat_add.data:
srr_task_form.condition.entries[i_iter].repeat.append_entry()
return render_template("admin/srr_task_add.html",
form=srr_task_form)
j_iter = 0
for rep in con.repeat.entries:
if rep.repeat_del.data:
srr_task_form.condition.entries[i_iter].repeat.entries.pop(
j_iter)
return render_template("admin/srr_task_add.html",
form=srr_task_form)
j_iter = j_iter + 1
i_iter = i_iter + 1
if srr_task_form.validate_on_submit():
data = srr_task_form.data
all_srr = []
srr_list = []
for con in data["condition"]:
srr_list.append([])
for each in con["repeat"]:
srr_list[-1].append(each['srr'])
all_srr.append(each['srr'])
all_srr = sorted(all_srr)
srr_id = "-".join(all_srr)
data_count = SrrTask.objects(_id=srr_id).count()
if data_count == 1:
flash("this srr_id is already exist !", "err")
return redirect(url_for("admin.srr_task_add"))
new_srr_task = SrrTask(_id=srr_id,
kegg_id=data["kegg_id"],
browse_link=data["browse_link"],
operon_path=data["operon_path"],
bw_path=data["bw_path"],
method=data["method"],
add_time=datetime.now())
new_srr_task.get_srr_nums(srr_list)
f = srr_task_form.operon_file.data
filename = secure_filename(f.filename)
save_path = os.path.join(data["operon_path"], "operon_file", filename)
if not os.path.exists(path):
os.system("mkdir " + path)
if not os.path.exists(os.path.join(path, "operon_file")):
os.system("mkdir " + os.path.join(path, "operon_file"))
f.save(save_path)
new_srr_task.get_operons_from_file(save_path)
new_srr_task.save()
flash("this srr_task is added !", "ok")
return redirect(url_for("admin.srr_task_add"))
return render_template("admin/srr_task_add.html", form=srr_task_form)
def srr_task(page=None):
if page is None:
page = 1
page_data = SrrTask.objects().paginate(page=page, per_page=10)
return render_template("admin/srr_task.html", page_data=page_data)
def index():
submit_form = SubmitForm()
if submit_form.condition_add.data:
submit_form.condition.append_entry()
return render_template("home/index.html", form=submit_form)
i_iter = 0
for con in submit_form.condition.entries:
if con.condition_del.data:
submit_form.condition.entries.pop(i_iter)
return render_template("home/index.html", form=submit_form)
if con.repeat_add.data:
submit_form.condition.entries[i_iter].repeat.append_entry()
return render_template("home/index.html", form=submit_form)
j_iter = 0
for rep in con.repeat.entries:
if rep.repeat_del.data:
submit_form.condition.entries[i_iter].repeat.entries.pop(j_iter)
return render_template("home/index.html", form=submit_form)
j_iter = j_iter + 1
i_iter = i_iter + 1
auto = ""
if submit_form.kegg_auto.data:
auto = "y"
if submit_form.kegg_not_auto.data:
auto = "n"
if submit_form.validate_on_submit():
data = submit_form.data
srr_list = []
all_srr = []
for con in data["condition"]:
srr_list.append([])
for each in con["repeat"]:
srr_list[-1].append(each['srr'])
all_srr.append(each['srr'])
all_srr = sorted(all_srr)
srr_id = "-".join(all_srr)
data_count = SrrTask.objects(_id=srr_id).count()
if data_count == 1:
return redirect(url_for("home.srr_id", _id=srr_id))
new_task_id = TaskId(task_id=str(uuid.uuid1()), srr_id=srr_id, email=data["email"], task_time=datetime.now())
new_task_id.save()
if submit_form.gff_file.data is not None:
gff = submit_form.gff_file.data
gff_filename = secure_filename(gff.filename)
gff_path = os.path.join(path, data["kegg_id"], gff_filename)
if not os.path.exists(path):
os.system("mkdir " + path)
if not os.path.exists(os.path.join(path, data["kegg_id"])):
os.system("mkdir " + os.path.join(path, data["kegg_id"]))
gff.save(gff_path)
fna = submit_form.fna_file.data
fna_filename = secure_filename(fna.filename)
fna_path = os.path.join(path, data["kegg_id"], fna_filename)
if not os.path.exists(os.path.join(path, data["kegg_id"])):
os.system("mkdir " + os.path.join(path, data["kegg_id"]))
fna.save(fna_path)
kegg_id = data["kegg_id"]
soft = data["software_select"]
method = data["method_select"]
corr = data["correlation_select"]
executor.submit(operon_predict, srr_list, kegg_id, soft, method, corr, srr_id)
return redirect(url_for("home.wait"))
return render_template("home/index.html", form=submit_form, auto=auto)
def srr_task_operon(_id=None, page=None):
if page is None:
page = 1
srr_task_query = SrrTask.objects(_id=_id).first()
page_data = srr_task_query.paginate_field("operon", page=page, per_page=50)
return render_template("home/srr_task_operon.html", page_data=page_data)