def blast_AmiGO(self, raw_sequence):
""" blast Amigo with data \
no customise blast parameters yet"""
query_blast = [
('action', 'blast'),
('seq', raw_sequence),
# ('seq_id','FB:FBgn0015946'),
('CMD', 'Put')]
self.web_page = web_page_utils.get_web_page(query_blast, AMIGO_BLAST_URL)
is_complete = self.web_page.find(MATCH_BLAST_NOT_COMPLETE)
previous = time.time()
while is_complete != -1:
current = time.time()
wait = previous + web_page_utils.DELAY - current
if wait > 0:
time.sleep(wait)
print("wait %d s" % web_page_utils.DELAY)
previous = current + wait
else:
previous = current
session_id_index = self.web_page.find(MATCH_BLAST_WAIT, is_complete) + MATCH_BLAST_WAIT_LEN
session_id_index_end = self.web_page.find(MATCH_BLAST_END, is_complete)
session_id = self.web_page[session_id_index:session_id_index_end]
query_wait = [
('action', 'get_blast_results'),
('session_id', session_id),
('CMD', 'Put')]
# http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi?action=get_blast_results&session_id=1284amigo1359406324&CMD=Put
self.web_page = web_page_utils.get_web_page(query_wait, AMIGO_BLAST_URL)
is_complete = self.web_page.find(MATCH_BLAST_NOT_COMPLETE)
def wait_for_query_result(query_wait):
query_page = web_page_utils.get_web_page(query_wait, AMIGO_BLAST_URL)
is_complete = query_page.find(MATCH_BLAST_NOT_COMPLETE)
# previous, current = [time.time()] * 2
previous = time.time()
while is_complete != -1:
current = time.time()
wait = previous + web_page_utils.DELAY - current
if wait > 0:
time.sleep(wait)
print("wait %d s" % web_page_utils.DELAY)
previous = current + wait
else:
previous = current
query_page = web_page_utils.get_web_page(query_wait, AMIGO_BLAST_URL)
is_complete = query_page.find(MATCH_BLAST_NOT_COMPLETE)
return query_page
def parse_querypage(self):
query_wait = parse_get_blast_results_query(self.session_id, 1)
self.query_page = wait_for_query_result(query_wait)
complete = False
# isReRun = self._get_seq_counter()
# def _get_seq_counter(self):
match = RE_NO_SEQ_COUNTER.search(self.query_page)
if match:
self.seq_counter = int(match.group(1))
if self.key_list and self.seq_counter != len(self.key_list):
warnings.warn("Mismatch numebr of sequencs=%d, and number of key=%d keys" % (self.seq_counter, len(self.key_list)))
if self.debug:
print "===DEBUG: Parsing %d sequences" % self.seq_counter
for page in range(self.seq_counter):
query = parse_get_blast_results_query(self.session_id, page + 1)
seq = None
while seq is None:
web_page = web_page_utils.get_web_page(query, AMIGO_BLAST_URL)
if web_page is not None:
seq = self.parse_seq(web_page)
# print "---in ", page, "with ", seq
self.go_results.append(seq)
complete = True
else:
"""
Error message from AmiGOs
fatal message There is an error in the configuration of AmiGO.
Your cached BLAST results were lost. Please try again.
"""
warnings.warn("No seq matched from id:%s!!! seq_counter=%d Recreate session_id!" % (self.session_id, self.seq_counter))
complete = False
# print self.session_id
self.session_id = None
while self.session_id is None:
self.create_session_id()
# print self.session_id
return complete
