def send_data(self, odrid):
try:
odr = self.__getodr(odrid)
fname = odr.filename
odr.close()
rconn = pyRserve.rconnect()
rconn.r.source("/home/avik/Desktop/yourMatch.R")
resp = rconn.r.classifyThis(fname)
respreader = csv.reader(open(fname + ".out.csv", 'rb'))
resp = {}
first = True
for row in respreader:
if first:
first = False
continue
resp[row[1]] = row[0]
self.wfile.write(json.dumps(resp))
del self.opendatarecords[odrid]
except IOError:
self.send_error(500, 'Unable to send/receive data to Rserve')
from Bio import SeqIO
from Bio.Alphabet import generic_dna
import subprocess
import pyRserve
fn = sys.argv[1]
times = 1
if len(sys.argv) > 2:
times = int(sys.argv[2])
# Start the RServer
subprocess.Popen([r"R", "CMD", "Rserve"], stdout=subprocess.PIPE).wait()
time.sleep(0.5)
conn = pyRserve.rconnect()
conn("library(GeneR)")
if verbose:
print >> sys.stderr, "Biopython translate ", fn, ":", times
for i in range(0, times):
if verbose:
print >> sys.stderr, i + 1
for seq_record in SeqIO.parse(fn, "fasta", generic_dna):
print ">", seq_record.id
ntseq = str(seq_record.seq)
print conn('strTranslate("' + ntseq + '")')
# Kill the RServer
subprocess.Popen([r"killall", "Rserve"], stdout=subprocess.PIPE)
