def blast(self): blast_exe = "/usr/bin/blastall" blast_program = "blastn" # if False and request.POST['fasta_filename1'] == request.POST['fasta_filename2'] : # session['flash'] = 'Files should not be identical successfully updated.' # session.save() # redirect_to(action='index',fasta_filename1=request.POST['fasta_filename1'],fasta_filename2=request.POST['fasta_filename2']) fasta_db = request.POST['fasta_filename1'] fasta_filename = request.POST['fasta_filename2'] blast_out = miniblast.blast_2_files(fasta_filename,fasta_db) blast_result_xml = miniblast.make_output_filename(fasta_filename,fasta_db) miniblast.save_results(blast_result_xml, blast_out) c.blast_results = miniblast.read_results(blast_result_xml ) # blast_out, error_handle = NCBIStandalone.blastall(blast_exe, blast_program, blast_db, blast_file) # records = NCBIXML.parse(blast_out) # c.results = [] # # while True: # try: # b_record = records.next() # c.results.append(b_record) # except StopIteration: # break return render('/miniblast/blast_miniblast.mako')
import sys sys.path.append("/home/kenglish/workspace/kenglish-ics699/www/biotoolspylons") from biotoolspylons.lib.base import * from biotoolspylons.model import fastafile from biotoolspylons.model import miniblast import Bio.Fasta from Bio.Blast import NCBIStandalone from Bio.Blast import NCBIXML fasta_db = "EST_Clade_A_1.fasta" fasta_filename = "EST_Clade_A_1.fasta" blast_out = miniblast.blast_2_files(fasta_filename, fasta_db) blast_result_xml = miniblast.make_output_filename(fasta_filename, fasta_db) miniblast.save_results(blast_result_xml, blast_out) blast_results = miniblast.read_results(blast_result_xml) record = blast_results[0] for attr in dir(record): print "%s = %s " % (attr, getattr(record, attr))