def attrs(objects, internals, mod, *attr):
for a in attr:
print a
g = getattr(A, a)
if hasattr(g, 'data'):
data = globals.json(getattr(g, 'data'), globals.datasource)
for o in objects.keys():
if not hasattr(g, 'data'):
if hasattr(g, 'args'):
args = getattr(g,'args')
mod.__getattribute__(getattr(g, 'fun'))(objects[o], args)
else:
mod.__getattribute__(getattr(g, 'fun'))(objects[o])
else:
if hasattr(g, 'args'):
args = getattr(g,'args')
mod.__getattribute__(getattr(g, 'fun'))(objects[o], data, args)
else:
mod.__getattribute__(getattr(g, 'fun'))(objects[o], data)
intermethods = [i for i in internals.__dict__.keys() if not i.startswith('_')]
apply(internal, [objects[o], internals] + sorted(intermethods))
def init(objects, clas, mod, types):
g = getattr(A, types)
data = globals.json(getattr(g, 'data'), globals.datasource)
for t in data:
objects[t] = clas(t)
def initall(objects, orfs, parset):
plist = globals.json(filehash[parset])
for par in plist:
objects[(par[0], par[1])] = paralogs((orfs[par[0]], orfs[par[1]]))
def init(objects, clas, types): data = globals.json(filehash[types], globals.datasource) for t in data: objects[t] = clas(t)
import simplejson
import globals
filehash = globals.json('Paralogsfilehash', './dbase/')
class paralogs:
def __init__(self, orfs):
self.orfs = orfs
def getalignindex(self):
if hasattr(self, 'alignment') and getattr(
self, 'alignment').keys().__len__() == 2:
print 'alignindex:' + str(self.orfs[0].orfname) + str(
self.orfs[1].orfname)
alignindex = {}
dashes = 0
i = 0
alignseq = getattr(self, 'alignment')
alignindex[self.orfs[0].orfname] = {}
while i < len(self.orfs[0].seq):
if alignseq[self.orfs[0].orfname][i + dashes] == '-':
dashes = dashes + 1
else:
alignindex[self.orfs[0].orfname][i] = dashes + i
i = i + 1
alignindex[self.orfs[1].orfname] = {}
i = 0
dashes = 0
while i < len(self.orfs[1].seq):
if alignseq[self.orfs[1].orfname][i + dashes] == '-':
import ORFs
import globals
def init(objects, clas, types):
data = globals.json(filehash[types], globals.datasource)
for t in data:
objects[t] = clas(t)
def attrs(objects, *attr):
for o in objects.keys():
for a in attr:
if 'args' in attrmethods[a].keys():
args = attrmethods[a]['args']
ORFs.__getattribute__(attrmethods[a]['fun'])(objects[o], args)
apply(internal, [objects[o]] + intermethods.keys())
def internal(obj, *internalattr):
for ia in internalattr:
obj.__class__.__dict__[intermethods[ia]](obj)
filehash = globals.json('./dbase/filehash')
attrmethods = globals.json('./dbase/attrmethods')
intermethods = globals.json('./dbase/intermethods')
if __name__ == '__main__':
orfs ={}
init(orfs, ORFs.Orf, 'geneset')
import simplejson
import Paralogs
import globals
"""
get wapinski paralogs, convert them to tupules, and add them as
attributes to the Paralog objects
"""
file = "paralogswapinskilistfigS6"
paraloglines = globals.json(file)
paraloglist = map(lambda x: x.strip("\n").split("\t"), paraloglines)
plist = [(x[0], x[1]) for x in paraloglist if x[0] in orfs.keys() and x[1] in orfs.keys()]
file = open("./data/DICparsalignment")
dicpars = simplejson.load(file)
file.close()
for p in Pars.keys():
if hasattr(Pars[p], "alignindex"):
setattr(Pars[p], "phosphosites", {})
for o in Pars[p].orfs:
if o in orfs.keys() and hasattr(orfs[o], "phosphosite"):
f = filter(lambda x: x in Pars[p].alignindex[o].keys(), orfs[o].phosphosite)
Pars[p].phosphosites[o] = map(lambda x: Pars[p].alignindex[o][x], f)
# add SYT positions
for p in Pars.keys():
if hasattr(Pars[p], "alignindex"):
def initall(objects, orfs, parset):
plist = globals.json(filehash[parset])
for par in plist:
objects[(par[0], par[1])] = paralogs((orfs[par[0]], orfs[par[1]]))
import simplejson
import globals
filehash = globals.json('Paralogsfilehash', './dbase/')
class paralogs:
def __init__(self, orfs):
self.orfs = orfs
def getalignindex(self):
if hasattr(self, 'alignment') and getattr(self, 'alignment').keys().__len__() == 2:
print 'alignindex:' + str(self.orfs[0].orfname) + str(self.orfs[1].orfname)
alignindex = {}
dashes = 0
i = 0
alignseq = getattr(self, 'alignment')
alignindex[self.orfs[0].orfname] = {}
while i < len(self.orfs[0].seq):
if alignseq[self.orfs[0].orfname][i+dashes] == '-':
dashes = dashes + 1
else:
alignindex[self.orfs[0].orfname][i] = dashes+i
i = i+1
alignindex[self.orfs[1].orfname] = {}
i = 0
dashes = 0
while i < len(self.orfs[1].seq):
if alignseq[self.orfs[1].orfname][i+dashes] == '-':
dashes = dashes + 1
else:
alignindex[self.orfs[1].orfname][i] = dashes+i
import simplejson
import Paralogs
import globals
'''
get wapinski paralogs, convert them to tupules, and add them as
attributes to the Paralog objects
'''
file = 'paralogswapinskilistfigS6'
paraloglines = globals.json(file)
paraloglist = map(lambda x: x.strip('\n').split('\t'), paraloglines)
plist = [(x[0], x[1]) for x in paraloglist if x[0] in orfs.keys() and x[1] in
orfs.keys()]
file = open('./data/DICparsalignment')
dicpars = simplejson.load(file)
file.close()
for p in Pars.keys():
if hasattr(Pars[p], 'alignindex'):
setattr(Pars[p], 'phosphosites', {})
for o in Pars[p].orfs:
if o in orfs.keys() and hasattr(orfs[o], 'phosphosite'):
f = (filter(lambda x: x in Pars[p].alignindex[o].keys(),
orfs[o].phosphosite))
Pars[p].phosphosites[o] = (map(lambda x: Pars[p].alignindex[o][x],
f))
# add SYT positions
