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msmBookKeeping.py
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#!/usr/bin/env python
"""
Collection of data bookkeeping functions and utilities for Hi-C analysis
Part of ChromaWalker package
"""
import numpy as np
import os
import sys
import cPickle as pickle
import hicFileIO as hfio
import dataFileReader as dfr
###########################################################
# Bookkeeping functions for reading MSM / TPT / target set data
def _get_tset_20160801(pars, tsetdict):
"""
Get selected target set from single chromosome.
"""
beta = pars.get('beta', 1.0)
ntarget = pars['ntarget']
key = (beta, ntarget)
if key not in tsetdict:
return []
else:
return tsetdict[key]
def _get_rho_20160801(pars, rhodict):
"""
Get selected target set rho from single chromosome.
"""
beta = pars.get('beta', 1.0)
ntarget = pars['ntarget']
key = (beta, ntarget)
if key not in rhodict:
return np.nan
rho = rhodict[key]
return rho
def _get_tsetReference_20180802(pars, ntarget):
"""
Get reference target set for pars['chrfullname'].
"""
tsetdatadir = pars['tsetdatadir']
tsetdataprefix = pars['tsetdataprefix']
region = pars.get('region', 'full')
res = pars['res']
resname = str(res / 1000) + 'kb'
chrfullname = pars['chrfullname']
tsetdataset = dfr._get_tsetdataset2(pars)
dirname = os.path.join(tsetdatadir, tsetdataprefix,
chrfullname, region, resname)
fname = os.path.join(dirname, tsetdataset +
'-reftsetdict_20160802.p')
tsetdict = hfio._pickle_secureread(fname, free=True)
if ntarget not in tsetdict:
print 'ntarget=%i not in reference: Using default reference.' % ntarget
return tsetdict['ref']
else:
return tsetdict[ntarget]
def _get_tsets_inter(pars, tsetdict):
"""
Get selected target sets from chromosome pair.
"""
region = pars.get('region', 'full')
beta = pars.get('beta', 1.0)
res = pars['res']
chrfullname1 = pars['chrfullname1']
chrfullname2 = pars['chrfullname2']
ntarget1 = pars['ntarget1']
ntarget2 = pars['ntarget2']
tsetdataset = dfr._get_tsetdataset2(pars)
key1 = (tsetdataset, chrfullname1, region, beta, res, ntarget1)
key2 = (tsetdataset, chrfullname2, region, beta, res, ntarget2)
tset1 = tsetdict[key1]
tset2 = tsetdict[key2]
return tset1, tset2
def _get_tsetmapkey(datadir, tset, norm='raw'):
"""
Get unique identifier used to label target sets on the same Hi-C array.
If tset is not currently mapped, give new ID.
"""
# Get and lock tsetmap
fname = os.path.join(datadir, 'tsetmap.p')
tsetmap = hfio._pickle_secureread(fname, free=False)
if tsetmap is None:
freed = True
tsetmap = {}
else:
freed = False
tsetindex = None
for index, (targetset, n) in tsetmap.iteritems():
if len(targetset) != len(tset):
continue
if not np.allclose(targetset, tset) and n == norm:
tsetindex = index
break
if tsetindex is None:
print 'Compute effective Laplacian...'
# Update dict
tsetindex = len(tsetmap)
tsetmap[tsetindex] = tset, norm
hfio._pickle_securedump(fname, tsetmap, freed=freed)
else:
# Remove lock
fname2 = fname + '-lock'
os.remove(fname2)
return tsetindex
#################################################
# To deprecate...
def _get_tset(pars, tsetdict):
"""
Get selected target set from single chromosome.
"""
region = pars.get('region', 'full')
beta = pars.get('beta', 1.0)
res = pars['res']
chrfullname = pars['chrfullname']
ntarget = pars['ntarget']
tsetdataset = dfr._get_tsetdataset2(pars)
key = (tsetdataset, chrfullname, region, beta, res, ntarget)
if key not in tsetdict:
return []
else:
return tsetdict[key]
def _get_rho(pars, rhodict):
"""
Get selected target set rho from single chromosome.
"""
region = pars.get('region', 'full')
beta = pars.get('beta', 1.0)
res = pars['res']
chrfullname = pars['chrfullname']
ntarget = pars['ntarget']
tsetdataset = dfr._get_tsetdataset2(pars)
key = (tsetdataset, chrfullname, region, beta, res, ntarget)
if key not in rhodict:
return np.nan
rho = rhodict[key]
return rho
def _get_tsetReference(pars, refdate='20160628'):
"""
Get reference target set (based on standardized optimal ntarget)
from single chromosome.
"""
tsetdatadir = pars['tsetdatadir']
region = pars.get('region', 'full')
beta = pars.get('beta', 1.0)
res = pars['res']
chrfullname = pars['chrfullname']
ntarget = pars['ntarget']
tsetdataset = dfr._get_tsetdataset2(pars)
key = (tsetdataset, chrfullname, region, beta, res, ntarget)
fname = os.path.join(tsetdatadir, 'ReferenceTsets-%s.p' % refdate)
if not os.path.isfile(fname):
print 'Reference tset data file %s not found!' % fname
sys.exit(1)
tsetdict = pickle.load(open(fname, 'rb'))
for k in tsetdict:
print k
tset = tsetdict[key]
return tset