def index(req):
try:
species1 = req.form.getfirst('sp1')
species2 = req.form.getfirst('sp2')
except:
return "<font color='red'>Please select species from both lists.</font>"
if species1 > species2:
species1, species2 = species2, species1
header = "block_no,block_score,e_value,locus_1,locus_2,ka,ks"
sql1 = "SELECT %s from block WHERE note='%s_%s' AND chr_1 is not NULL AND chr_2 is not NULL" % (header, species1, species2)
results = myconnect(sql1)
if results==-1: return DB_FAIL_MSG
# write to intermediate file
os.chdir("/var/www/duplication/usr/")
file_name = "%s_%s_block.csv.gz" % (species1, species2)
if not os.path.exists(file_name):
import gzip
f = gzip.open(file_name, "wb")
f.write(header + "\n")
for r in results:
f.write(",".join(str(x) for x in r) + "\n")
f.close()
return "%d records found. Transferring data ..." % len(results)
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from pylab import *
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from preferences import myconnect
import itertools
import os
# generate data file
sql = "SELECT note, ks FROM block"
results = list(myconnect(sql))
results.sort()
fontdict = {"color":"b", "fontweight":"bold", "size":10}
def my_hist(l, interval, max_r, c):
n = []; p = []
total_len = len(l)
if total_len==0: return 0
for i in arange(0, max_r, interval):
xmin, xmax = i-.5*interval, i+.5*interval
nx = [x for x in l if xmin<=x<xmax]
n.append(i)
p.append(len(nx)*100./total_len)
ax.set_xlabel('Synonymous substitutions per site (Ks)', fontdict)
ax.set_ylabel('Percentage of %d gene pairs'%total_len, fontdict)
def index(req):
q = req.form.getfirst("term")
query = "SELECT locus FROM loci WHERE locus LIKE '%s%%' ORDER by locus limit 5" % q
res = myconnect(query)
return json.dumps([x[0] for x in res])