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))
