def index(self, format='html'):
"""GET /fastas: All items in the collection."""
c.fasta_files = fastafile.get_fasta_files()
# for filename in os.listdir(permanent_store):
# if re.compile('.*fasta$').match(filename):
# c.fasta_files.append( filename )
# c.links = [ 'James', 'Ben', 'Philip' ]
return render('/fastas/index_fasta.mako')
def index(self, format='html'):
"""GET /flexfastas: All items in the collection."""
# url_for('flexfastas')
message = "They called index on flexfastas"
log.debug(message)
response.headers['Content-type'] = "text/xml"
c.fasta_files = fastafile.get_fasta_files()
return render('/flexfastas/index_flexfasta.xml.mako')
import sys
sys.path.append('/home/kenglish/workspace/kenglish-ics699/www/biotoolspylons')
#sys.path.append('/home/kenglish/workspace/kenglish-ics699/sandbox/blast_tests')
from biotoolspylons.lib.base import *
from biotoolspylons.model import fastafile
from biotoolspylons.model import miniblast
from biotoolspylons.model.pathinfo import *
#import Bio.Fasta
#from Bio.Blast import NCBIStandalone
#from Bio.Blast import NCBIXML
#
files = fastafile.get_fasta_files()
for file in files:
print file.path
print file.size
# fileinfo = PathInfo(file)
# print fileinfo
#p = PathInfo("/home/kenglish/downloads/uploads/EST_Clade_A_1.fasta")
#print p
def index(self):
# Return a rendered template
# return render('/some/template.mako')
# or, Return a response
c.fasta_files = fastafile.get_fasta_files()
return render('/miniblast/index_miniblast.mako')
def test_fastfile():
files = fastafile.get_fasta_files()
assert files[0].filename
assert files[0].size
assert files[0].to_xml()