def main(in_args):
wsdl_url = "http://v2.topcons.net/pred/api_submitseq/?wsdl"
fixtop = ""
if os.path.isfile(in_args.input):
try:
seqbuddy = Sb.SeqBuddy(in_args.input, out_format="fasta")
Sb.clean_seq(seqbuddy)
# Sb.hash_ids(seqbuddy)
except br.GuessError:
print("Unable to read the provided input file, is it a properly formatted sequence file?")
return 1
if len(str(seqbuddy)) >= MAX_FILESIZE:
print("You input seqfile is too large! Please split the file into chunks less than %d Mb."
% MAX_FILESIZE_IN_MB, file=sys.stderr)
return 1
# ***** Here's the meat ***** #
myclient = Client(wsdl_url, cache=None)
ret_value = myclient.service.submitjob(str(seqbuddy), fixtop, in_args.jobname, in_args.email)
if len(ret_value) >= 1:
jobid, result_url, numseq_str, errinfo, warninfo = ret_value[0][:5]
if jobid != "None" and jobid != "":
print("You have successfully submitted your job with %s sequences. jobid = %s" % (numseq_str, jobid))
if warninfo != "" and warninfo != "None":
print("Warning message:\n%s" % warninfo)
else:
print("Failed to submit job!")
if errinfo != "" and errinfo != "None":
print("Error message:\n%s" % errinfo)
if warninfo != "" and warninfo != "None":
print("Warning message:\n%s" % warninfo)
else:
print("Failed to submit job!")
return 1
else:
myclient = Client(wsdl_url, cache=None)
ret_value = myclient.service.checkjob(in_args.input)
if len(ret_value) >= 1:
status, result_url, errinfo = ret_value[0][:3]
if status == "Failed":
print("Your job with jobid %s is failed!" % in_args.input)
if errinfo != "" and errinfo != "None":
print("Error message:\n%s" % errinfo)
elif status == "Finished":
print("Your job with jobid %s is finished!" % in_args.input)
if not os.path.exists(in_args.outpath):
try:
os.makedirs(in_args.outpath)
except OSError:
print("Failed to create the outpath %s" % in_args.outpath)
return 1
outfile = "%s/%s.zip" % (in_args.outpath, in_args.input)
if not os.path.exists(outfile):
print("Retrieving")
urllib.request.urlretrieve(result_url, outfile)
if os.path.exists(outfile):
print("The result file %s has been retrieved for jobid %s" % (outfile, in_args.input))
else:
print("Failed to retrieve result for jobid %s" % in_args.input)
with zipfile.ZipFile(outfile) as zf:
zf.extractall(in_args.outpath)
with open("%s/%s/query.result.txt" % (in_args.outpath, in_args.input), "r") as ifile:
topcons = ifile.read()
topcons = topcons.split("##############################################################################")[2:-1]
records = []
for rec in topcons:
seq_id = re.search("Sequence name: (.*)", rec).group(1).strip()
seq = re.search("Sequence:\n([A-Z]+)", rec).group(1).strip()
alignment = ""
for algorithm in ["TOPCONS", "OCTOPUS", "Philius", "PolyPhobius", "SCAMPI", "SPOCTOPUS"]:
try:
top_file = re.search("%s predicted topology:\n([ioMS]+)" % algorithm, rec).group(1).strip()
alignment += ">%s\n%s\n\n" % (algorithm, top_file)
except:
print("%s: %s" % (seq_id, algorithm))
pass
alignment = Alb.AlignBuddy(alignment)
# print(alignment)
Alb.consensus_sequence(alignment)
cons_seq = Sb.SeqBuddy(">%s\n%s\n" % (seq_id, seq), out_format="genbank")
counter = 1
for tmd in re.finditer("([MX]+)", str(alignment.records()[0].seq)):
Sb.annotate(cons_seq, "TMD%s" % counter, "%s-%s" % (tmd.start(), tmd.end()))
counter += 1
records.append(cons_seq.records[0])
seqbuddy = Sb.SeqBuddy(records, out_format="genbank")
seqbuddy.write("%s/%s.gb" % (in_args.outpath, in_args.input))
elif status == "None":
print("Your job with jobid %s does not exist! Please check you typing!" % in_args.input)
else:
print("Your job with jobid %s is not ready, status = %s" % (in_args.input, status))
else:
print("Failed to get job!")
return 1
return 0
def test_weighted_consensus(alb_resources, hf, key, next_hash):
tester = Alb.consensus_sequence(alb_resources.get_one(key))
assert hf.buddy2hash(tester) == next_hash
def test_consensus_error(alb_resources, hf):
tester = alb_resources.get_one('o d f')
with pytest.raises(ValueError) as err:
Alb.consensus_sequence(tester, mode="foo")
assert "No valid consensus" in str(err)
def test_simple_consensus(alb_resources, hf, key, next_hash):
tester = Alb.consensus_sequence(alb_resources.get_one(key), "simple")
assert hf.buddy2hash(tester) == next_hash
