def __init__(self,name,dirname,fname,fans):
# name is used as log file name
# dirname is location saving log file
self._name = name
self._dir = dirname
#pssm = pssm2feature2.pssm(fname)
self._starts = {idch:start for idch,start,seq in seq2feature.fasta2seq(fname)}
if fans is not None:
self._ans = util.ans(fans)
import os
import random
import util
from core import seq2feature
#DIR = "/net2/presto-users/masaki070540/code/xbind/"
DIR = "./"
log_path = lambda name,window,c,g,no,idch:DIR + "tmp/svm/fold_whole/%s.%s.%s.%s.log.%s/%s.log" % (
name,window,c,g,no,idch)
starts = lambda fname:{idch:start for idch,start,seq in seq2feature.fasta2seq(fname)}
def _readliner(line):
rec = line.strip().split()
idch = rec[0].split(':')[0]
val = float(rec[2])
return idch,val
def iter_desc(name,window,c,g,idch):
fname = get_log(name,window,c,g,idch)
# For get_log() bagg. ( Test didn't execute using All proteins.
if fname is not None:
with open(fname) as fp:
for idch,val in (_readliner(line) for line in iter(fp.readline,"")):
yield val
def get_log(name,window,c,g,idch):
for no in range(5):
if os.path.exists(log_path(name,window,c,g,no,idch)):
def __init__(self,name,dirname,fname):
valid.__init__(self,name,dirname)
self._starts = {idch:start for idch,start,seq in seq2feature.fasta2seq(fname)}
def __init__(self, name, dirname, fname):
valid.__init__(self, name, dirname)
self._starts = {
idch: start
for idch, start, seq in seq2feature.fasta2seq(fname)
}