def report_check_res(ins_dict,path_dict):
import draw_plasmid as dp
vector_path_gb=path_dict["vector_path_gb"]
vector_rep_seq=str(dp.plasmid(vector_path_gb).record.seq)
re_names=ins_dict["vec_re_names"]+\
[ins_dict["utr_5_re_name"]]+[ins_dict["utr_3_re_name"]]
repeat_list=[]#record the repeat enzymes
for re_name in set(re_names):
re_seq=re.sub(r"'","",RE_dict[re_name])
re_pattern=dp.deg_pattern(re_seq)
if re.search(re_pattern,vector_rep_seq,re.I):
repeat_list.append(re_name)
if repeat_list:
return "warning","The restriction enzymes used to build the construct.",\
"The REs you have used are %s."%", ".join(set(re_names)),\
"%s still exist in your construct, please be careful."%", ".join(repeat_list)
else:
return "check","The restriction enzymes used to build the construct.",\
"The REs you have used are %s."%", ".join(set(re_names)),\
"None of them will cut your construct, it is safe to use."
user_name="test_user"
if form.has_key("advance"):
modi_headline=change_headline_color(modi_headline_list[0])\
+modi_headline_list[1]+modi_headline_list[2]
button_name="goto_advance"
else:
modi_headline=change_headline_color(modi_headline_list[0])\
+modi_headline_list[2]
button_name="goto_review" #decide whether to go to advanced mode
vector_path=form["vector"].value
task_name=form.getvalue("task_name")
ins_name=form.getvalue("ins_name")
vec_name=re.search(r'.+/(.+?)\.gb$',vector_path).group(1)
out_path="tmp/"+user_name+"___"+re.sub(r"\.","",str(time.time()))+"/"
os.mkdir(out_path)
vector_um=dp.plasmid(vector_path,out_path=out_path,step_name="goto_modification")#vector_um:unmodified vector
# open("./"+"test.txt","w").write(str(vector_um.get_mcs()))
mcs_dict=vector_um.get_mcs()
mcs_path=vector_um.draw_mcs()
vector_um.organize()
mcs_ac=[]
for start_pos,end_pos,RE_name,RE_seq in mcs_dict["RE_list"]:
RE_seq=re.sub("'","|",vector_um.RE_dict[RE_name])
mcs_ac.append(dict(value=str(start_pos),
label=str(start_pos)+": "+RE_name+"("+RE_seq+")",
desc=RE_name+"("+RE_seq+")"))
mcs_dict["mcs_ac"]=sorted(mcs_ac,key=lambda x:int(x["value"]))
vector_um_path= vector_um.draw()#this function returns the path of figure
if not form["5utr"].value:
utr_5=""
