Python get_fasta_files Examples

Example #1

File: fastas.py Project: kenglishhi/kenglish-ics699

    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')

Example #2

File: flexfastas.py Project: kenglishhi/kenglish-ics699

 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')

Example #3

File: filestest.py Project: kenglishhi/kenglish-ics699

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

Example #4

File: miniblast.py Project: kenglishhi/kenglish-ics699

 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')

Example #5

File: test_fastafile.py Project: kenglishhi/kenglish-ics699

def test_fastfile():
    files = fastafile.get_fasta_files()
    assert files[0].filename
    assert files[0].size
    assert files[0].to_xml()