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'))