def index():
query = request.GET.get('q')
if query:
session = Session(SESSION_DIR)
session.save()
return template('uniprot_progress', session=session, query=query)
else:
return template('uniprot_form')
from proteins.session import Session
record = Session.search_prot('paltanavicius')
import pdb
pdb.set_trace()
# from Bio.Blast import NCBIWWW, NCBIXML
# from Bio import ExPASy, SwissProt
#
# handle = ExPASy.sprot_search_ful('8332116')
#
# import pdb
# pdb.set_trace()
# record = SwissProt.read(handle) # E: ValueError
#
# import pdb
# pdb.set_trace()
# result_handle = NCBIWWW.qblast("blastn", "nr", "8332116")
# blast_record = NCBIXML.read(result_handle)
# result_handle.close()
#
# E_VALUE_THRESH = 0.04
#
# for alignment in blast_record.alignments:
# for hsp in alignment.hsps:
# if hsp.expect < E_VALUE_THRESH:
# print '****Alignment****'
# print 'sequence:', alignment.title
# print 'length:', alignment.length
def regenerate_blast(id):
session = Session(SESSION_DIR, id)
session.create_blast_report()
redirect(session.get_url())
def blast(id, accession):
session = Session(SESSION_DIR, id)
session.search_blast(accession)
session.create_blast_report()
redirect(session.get_url())
def uniprot(id):
query = request.GET['q']
session = Session(SESSION_DIR, id)
session.search_uniprot(query)
session.create_accession_report()
redirect(session.get_url('accessions'))
