def plotCrossValidation():
"main figure subplot with corss-validation"
matplotlib.rcParams['font.sans-serif'] = 'Arial'
plt.figure(figsize=(1, 1))
FG = HiCdataset(workingFile1, myGenome)
FG.load(GMFrag)
Tanay = binnedData(1000000)
Tanay.simpleLoad("GM-all-10p", "GM-1")
#need to create these datasets using fragment-level analysis
Tanay.simpleLoad("GM-all-90p", "GM-9")
Tanay.removePoorRegions()
Tanay.iterativeCorrectWithSS()
Tanay.removeZeros()
b1, b2 = (Tanay.biasDict["GM-1"], Tanay.biasDict["GM-9"])
cPickle.dump((b1, b2), open("CrossValidatioN", 'wb'))
ax = plt.gca()
b1, b2 = cPickle.load(open("CrossValidatioN", 'rb'))
print cr(b1, b2)
plt.scatter(b1, b2, s=.7, color="k", linewidth=0)
plt.xlabel(r"10% reads", fontsize=8)
plt.ylabel(r"90% reads", fontsize=8)
plt.xlim((0, 1.5))
plt.ylim((0, 1.5))
plt.xticks([0, 0.5, 1, 1.5])
plt.yticks([0, 0.5, 1, 1.5])
removeAxes(shift=0)
fs = 6
for xlabel_i in ax.get_xticklabels():
xlabel_i.set_fontsize(fs)
for xlabel_i in ax.get_yticklabels():
xlabel_i.set_fontsize(fs)
plt.show()
def getScaling(self):
HD = HiCdataset(self.refined,
self.getGenomeObject(),
self.getEnzyme(),
1000,
mode='r',
tmpFolder="\tmp",
dictToStoreIDs="h5dict")
scal = HD.plotScaling(excludeNeighbors=2, normalize=True, mindist=2000)
return scal
def getFrags():
"""
A method that calculates a set of restriction fragments covered in all hg19, or in all mm9 datasets
Used for the correct calculation of scalings
"""
mouse = "/home/magus/HiC2011/DrosophilaSingleCell2015/alternativeFiltering/mm9/oocyte_combined_refined.frag"
human = "/home/magus/HiC2011/DrosophilaSingleCell2015/alternativeFiltering/hg19/K562_combined_refined.frag"
a = HiCdataset("bla", os.path.join("../../data/hg19"), enzymeName=1000, inMemory=True)
a.load(human)
humanFrags = a.fragmentSum() > 0
a = HiCdataset("bla", os.path.join("../../data/mm9"), enzymeName=1000, inMemory=True)
a.load(mouse)
mouseFrags = a.fragmentSum() > 0
return humanFrags, mouseFrags
def getByChromosomeScaling(self):
HD = HiCdataset(self.refined,
self.getGenomeObject(),
self.getEnzyme(),
1000,
mode='r',
tmpFolder="\tmp",
dictToStoreIDs="h5dict")
scals = {}
for chrom in range(self.getGenomeObject().chrmCount):
for arm in [0, 1]:
if arm == 0:
region = (chrom, 0, self.genomeObject.cntrMids[chrom])
else:
region = (chrom, self.genomeObject.cntrMids[chrom],
self.genomeObject.chrmLens[chrom])
scal = HD.plotScaling(excludeNeighbors=2,
normalize=True,
mindist=2000,
regions=[region])
scals[(chrom, arm)] = scal
return scals
def doScaling(dataset):
genome = os.path.split(os.path.split(dataset)[0])[-1]
a = HiCdataset("bla", os.path.join("../../data/", genome), enzymeName=1000, inMemory=True)
a.load(dataset)
# a.load("../hadjurCohesin2012/mm9/AST-WT-AdCre-R1-Hi ndIII_refined.frag")
a.maskFilter((a.chrms1 == a.chrms2) * (a.strands1 == a.strands2))
sc = {}
regions = []
regions2 = []
for chromosome in range(0, a.genome.chrmCount):
cur = [(chromosome, 0, a.genome.cntrMids[chromosome]),
(chromosome, a.genome.cntrMids[chromosome],
a.genome.chrmLens[chromosome])]
if chromosome % 2 == 0:
regions += cur
else:
regions2 += cur
frags = fragdict[genome]
sc1 = a.plotScaling(excludeNeighbors=2, mindist=6000, regions=regions, plot=False, fragids1=frags, fragids2=frags)
sc2 = a.plotScaling(excludeNeighbors=2, mindist=6000, regions=regions2, plot=False, fragids1=frags, fragids2=frags)
sc3 = a.plotScaling(excludeNeighbors=2, mindist=6000, regions=regions + regions2, plot=False, fragids1=frags, fragids2=frags)
return sc1, sc2, sc3
#filenames = [j for j in os.listdir(path) if j.endswith("SC35-R1-HaeIII_merged.frag")]
filenames = [j for j in os.listdir(path) if j.endswith("_refined.frag")]
genomeName="hg19"
genome_db = getGenome(genomeName)
for fl in sorted(filenames):
print fl
out_file = path + fl.split("_refined.frag")[0] + "_refined_wo_man_dupl"
f1 = HiCdataset(path + fl.split("_refined.frag")[0] + "_refined_wo_man_dupl.frag",enzymeName = enzyme,
genome=getGenome(workingGenome),tmpFolder = "tmp",dictToStoreIDs="h5dict",
mode='w')
f1.load(path + fl)
#f1 = mirnylib.h5dict.h5dict(path + fl ,'r+')
print len(f1.chrms1)
cuts1 = list(f1.cuts1)
cuts2 = list(f1.cuts2)
chrms1 = list(f1.chrms1)
import subprocess
import argparse
import sys
from mirnylib.genome import Genome
from hiclib.fragmentHiC import HiCdataset
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Sort contacts by position and order the reads of each pair so that all "
"contacts are upper triangular with respect to the chromosome ordering "
"given by the chromsizes file."
)
parser.add_argument("genome", help="hiclib genome path", metavar="GENOME_PATH")
parser.add_argument("pairs", help="HDF5 hiclib read pairs file", metavar="PAIRS_PATH")
args = vars(parser.parse_args())
genome_db = Genome(args["genome"])
infile = args["pairs"]
if args["out"] is not None:
outfile = args["out"]
ds = HiCdataset(outfile, genome_db, "HindIII")
ds.load(infile)
ds._sortData()
else:
outfile = args["out"]
ds = HiCdataset(infile, genome_db, "HindIII")
ds._sortData()
def plotFigure2c():
TR = HiCdataset()
TR.load("GM-all.refined")
hm = TR.buildHeatmap(1, 1, 1000000, False, False)
TR.calculateWeights()
TR.weights = np.ones(len(TR.weights), float) # if you want to correct just by fragment density, not by length dependence
hm2 = TR.buildHeatmap(1, 1, 1000000, False, weights=True)
hm2[np.isnan(hm2)] = 0
mask = np.sum(hm, axis=0) > 0
"""p1-6 are 6 lines to be plotted, below is plotting only"""
p1 = np.sum(hm, axis=0)[mask]
p3 = np.sum(correct(hm), axis=0)[mask]
p5 = np.sum(ultracorrect(hm, 40), axis=0)[mask]
p4 = np.sum(correct(hm2), axis=0)[mask]
p2 = np.sum(hm2, axis=0)[mask]
p6 = np.sum(ultracorrect(hm2, 40), axis=0)[mask]
matplotlib.rcParams['font.sans-serif'] = 'Arial'
dashstyle = (3, 3)
plt.figure(figsize=(4, 4))
ax = plt.subplot(2, 1, 1)
plt.xlim((0, 80))
plt.ylim((0, 2))
plt.ylabel("Total coverage", fontsize=8)
line21 = plt.plot(p1 / p1.mean(), "-", linewidth=1, color="#e5a826")[0]
line22 = plt.plot(
p3 / p3.mean(), "--", linewidth=1, color="#e5a826")[0]
line22.set_dashes(dashstyle)
line23 = plt.plot(p5 / p5.mean(), linewidth=1, color="grey")[0]
for xlabel_i in ax.get_xticklabels():
xlabel_i.set_fontsize(8)
for xlabel_i in ax.get_yticklabels():
xlabel_i.set_fontsize(8)
legend = plt.legend([line21, line22, line23],
["Raw data", "Single correction", "Iterative correction"], prop={"size": 6}, loc=1, handlelength=2)
legend.draw_frame(False)
removeAxes(shift=0, ax=ax)
for i in ax.spines.values():
i.set_color('none')
ax.axhline(linewidth=1, color='black')
ax.axvline(linewidth=1, color='black')
ax2 = plt.subplot(2, 1, 2, sharex=ax)
plt.xlim((0, 80))
plt.ylim((0, 2))
plt.xlabel("Position on chom 1 (MB)", fontsize=8)
plt.ylabel("Total coverage", fontsize=8)
line1 = plt.plot(p4 / p4.mean(), "--", color="#9b3811", linewidth=1)[0]
line1.set_dashes(dashstyle)
line2 = plt.plot(p2 / p2.mean(), "-", color="#9b3811", linewidth=1)[0]
line3 = plt.plot(p6 / p6.mean(), linewidth=1, color="grey")[0]
for xlabel_i in ax2.get_xticklabels():
xlabel_i.set_fontsize(8)
for xlabel_i in ax2.get_yticklabels():
xlabel_i.set_fontsize(8)
legend = plt.legend([line2, line1, line3],
["HindIII corrected", "Single correction", "Iterative correction"], prop={"size": 6}, loc=1, handlelength=2)
legend.draw_frame(False)
removeAxes(shift=0, ax=ax2)
plotting.niceShow()
import numpy
np = numpy
from mirnylib import genome
from mirnylib.numutils import adaptiveSmoothing, trunc, ultracorrect
from mirnylib.h5dict import h5dict
genomeDb = genome.Genome('../data/caul',
chrmFileTemplate="%s.fa",
readChrms=[])
for expName in os.listdir(
"caul"): # this directory contains folders with names of experiments.
# data will be loaded from different folders
TR = HiCdataset(
"bla",
genome=genomeDb,
inMemory=True,
) # inMemory, as data are small (<1e8 reads)
TR.load("data/" + expName + "_refined.frag") # load filtered data
# Now save all heatmaps with different resolutions, etc.
TR.saveHeatmap("data/" + expName + "-5k_overlap.hm",
5000,
useFragmentOverlap=True)
TR.saveHeatmap("data/" + expName + "-10k_overlap.hm",
10000,
useFragmentOverlap=True)
TR.saveHeatmap("data/" + expName + "-20k_overlap.hm",
20000,
useFragmentOverlap=True)
TR.saveHeatmap("data/" + expName + "-50k.hm", 50000)
from mirnylib.systemutils import fmap,setExceptionHook
from mirnylib.genome import Genome
import numpy as np
import os
import sys
genomeName = "GalGal5filtered"
genome_db = Genome("/mnt/storage/home/vsfishman/HiC/fasta/GalGal5/GCF_000002315.4_Gallus_gallus-5.0_assembly_structure/Primary_Assembly/galGal5_all_contigs.filtered/",
readChrms=[],
chrmFileTemplate="N%s.fa")
basefolder = "/mnt/storage/home/vsfishman/HiC/data/chick/mapped-GalGal5filtered/B1_TTAGGC_L001_/"
filename = "chunk0001.hdf5"
TR = HiCdataset(basefolder+filename+".HiCdataset", genome=genome_db,
maximumMoleculeLength=500,enzymeName = "HindIII",tmpFolder = "tmp",
mode='w') # remove inMemory if you don't have enough RAM
TR.parseInputData(dictLike=basefolder+filename)
TR.filterDuplicates()
TR.filterLarge(10000,10)
TR.filterExtreme(cutH=0.001, cutL=0)
TR.writeFilteringStats()
TR.printMetadata(saveTo=basefolder+filename+".stat")
TR.saveHeatmap(basefolder+filename+".hm-res-1000kb",1000000)
comment ="""
#------------------------End set of filters applied----------
print("----->Building Raw heatmap at different resolutions")
TR.printStats()
for res in wholeGenomeResolutionsKb:
TR.saveHeatmap(out_file + "-{0}k.hm".format(res), res*1000)
#Now merging different experiments alltogether
#note that the first column is not here, as it is a replica
experiments = set([(i[0], i[2], i[3]) for i in combinedExperimentNames])
print experiments
for experiment in experiments:
workingGenome = experiment[1]
myExperimentNames = [
i[1] + "_refined.frag" for i in combinedExperimentNames
if (i[0], i[2], i[3]) == (experiment[0], experiment[1], experiment[2])
]
assert len(myExperimentNames) > 0
if len(myExperimentNames) > 1:
#If we have more than one experiment (replica) for the same data, we can combine.
TR = HiCdataset(os.path.join(
workingGenome,
"%s-all-%s_refined.frag" % (experiment[0], experiment[2])),
genome=genomeFolder(workingGenome))
statSaveName = os.path.join(
"statistics", workingGenome,
"%s-all-%s_refined.stat" % (experiment[0], experiment[2]))
TR.merge(myExperimentNames)
TR.printMetadata(saveTo=statSaveName)
for res in wholeGenomeResolutionsKb:
TR.saveHeatmap(
os.path.join(
workingGenome, "%s-all-%s-{0}k.hm" %
(experiment[0], experiment[2])).format(res), res * 1000)
for res in byChromosomeResolutionsKb:
TR.saveByChromosomeHeatmap(
os.path.join(
from mirnylib.genome import Genome
import os
resolution = 10000
genomeName = "mm10"
genome_db = Genome("/mnt/storage/home/vsfishman/HiC/fasta/" + genomeName,
readChrms=["#", "X", "Y"])
data_folder = "/mnt/storage/home/vsfishman/HiC/data/mESC/mapped-mm10/mm10/"
fdataset_fname = "mESC-all-NcoI_refined.frag"
setExceptionHook()
print "Loading HiCdataset"
TR = HiCdataset(data_folder + fdataset_fname,
enzymeName="HindIII",
mode='r',
genome=genome_db)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "_res"+ "1000k.hm", 1000000)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "_res"+ "40k.hm", 40000)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "_res" + "10k.hm", 10000,useFragmentOverlap=True)
for resolution in [10000, 25000]:
print "Saving heatmap"
TR.saveHiResHeatmapWithOverlaps(
data_folder + fdataset_fname + "_res" + str(resolution / 1000) +
"k_hiRes.hm", resolution)
#TR.saveByChromosomeHeatmap(data_folder + fdataset_fname + "_res" + str(resolution/1000)+"k_bychr.hm", resolution=resolution,includeTrans=True)
out.write(f.split(".")[0] + "\t" + str(chr_len) + "\n")
else:
for i in xrange(genome_db.chrmCount):
if genome_db.chrmCount > 100:
out.write("N" + genome_db.idx2label[i] + "\t" +
str(genome_db.chrmLens[i]) + "\n")
else:
out.write(genome_db.idx2label[i] + "\t" +
str(genome_db.chrmLens[i]) + "\n")
out.close()
#Step 2. Load fragments and save it in juicybox format
Fr = HiCdataset(fr_daraset + ".tmp" + str(random.randint(0, 10000)),
enzymeName=enzyme,
mode='w',
genome=genome_db,
inMemory=True)
Fr.load(fr_daraset)
out = open(out_file_prefix + ".contacts", "w")
print "Reporting ", Fr.N, " contacts"
dotsize = Fr.N / 500
print "one dot is ", dotsize, " contacts"
strands1 = np.array(Fr._getVector("strands1"), dtype=np.int8)
cuts1 = np.array(Fr._getVector("cuts1"), dtype=np.uint64)
chrms1 = np.array(Fr._getVector("chrms1"), dtype=np.uint16)
fragids1 = np.array(Fr._getVector("rfragAbsIdxs1"), dtype=np.uint32)
strands2 = np.array(Fr._getVector("strands2"), dtype=np.int8)
def refine_dataset(filenames, niceval, delete=True, parse_in_memory=True):
"""
Map the fragments from each replicate to chromosomes (in parallel)
Parameters
----------
filenames[0] is a list of filenames of incoming files
filenames[1] is a folder for outgoing file
filenames[2] is a working genome, that is output directory
filenames[3] is an enzyme for a given experiment
create : bool, optional
If True, parse each file.
If False, assume that files were already parsed
(e.g. if you are just playing around with filtering parameters)
delete : bool, optional
If True, delete parsed files after merging.
Man, these files may be huge... if you don't have a 10TB RAID, this may be useful.
parseInMemory : bool, optional
Perform parsing input files in memory.
"""
in_files = filenames[0]
out_file = filenames[1]
stat_folder = os.path.join("statistics", out_file)
working_genome = filenames[2]
enzyme = filenames[3]
nice_list = [niceval for i in in_files]
parse_list = [parse_in_memory for i in in_files]
genome_list = [working_genome for i in in_files]
enzyme_list = [enzyme for i in in_files]
stat_folder_list = [stat_folder for i in in_files]
#map(parse_onename, in_files)
Parallel(n_jobs=20)(delayed(parse_mapped_reads)(infile, nice_val, genome, enzyme, stat_folder, parse_val) for infile, nice_val, genome, enzyme, stat_folder, parse_val in
zip(in_files, nice_list, genome_list, enzyme_list, stat_folder_list, parse_list))
# Merge in all parsed files from one experiment
print("Merging files all together, applying filters...")
TR = HiCdataset(ensure(out_file + "_merged.frag"),
genome=genomeFolder(working_genome), enzymeName=enzyme, tmpFolder="tmp", dictToStoreIDs="h5dict",
mode="w")
TR.merge([i + "_parsed.frag" for i in in_files])
if delete: # cleaning up parsed files
for delFile in [i + "_parsed.frag" for i in in_files]:
os.remove(delFile)
print("done!")
print("Filtering merged data...")
TR = HiCdataset(out_file + "_refined.frag", enzymeName=enzyme,
genome=genomeFolder(working_genome), tmpFolder="tmp", dictToStoreIDs="h5dict",
mode='w')
TR.load(out_file + "_merged.frag")
# ----------------------------Set of filters applied -------------
TR.filterDuplicates()
TR.filterLarge(10000, 10)
TR.filterExtreme(cutH=0.001, cutL=0)
TR.writeFilteringStats()
TR.printMetadata(saveTo=stat_folder + ".stat")
print("done!")
# ------------------------End set of filters applied----------
print("Building heatmaps at specified resolutions...")
TR.printStats()
for res in whole_genome_resolutions_Kb:
TR.saveHeatmap(out_file + "-{0}k.hm".format(res), res * 1000)
for res in by_chromosome_resolutions_Kb:
TR.saveByChromosomeHeatmap(out_file + "-{0}k.byChr".format(res), res * 1000)
for res in hi_res_with_overlap_resolutions_Kb:
TR.saveHiResHeatmapWithOverlaps(out_file + "-{0}k_HighRes.byChr".format(res), res * 1000)
for res in super_hi_res_with_overlap_resolutions_Kb[:-skip]:
TR.saveSuperHighResMapWithOverlaps(out_file + "-{0}k_HighRes.byChr".format(res), res * 1000)
print("done!")
def parse_mapped_reads(onename, niceval, working_genome, enzyme, stat_folder, in_memory):
"""
Parse the given h5 mapped reads, output to a partial fragment file.
:param onename: (string) the name of this fragment
:param niceval: (int) positive int to rank the priority of this job
:param working_genome: (string) name of the genome aganist which we mapped the reads
:param enzyme: (string) name of the restriction enzyme used to cut fragments
:param stat_folder: (string) folder in which to write fragment mapping stats
:return: none explicit, h5 file is saved to disk
"""
# set the niceness of this sub-process:
os.nice(niceval)
np.random.seed()
# Parsing individual files, either in memory or on disk
if in_memory:
finalname = onename + "_parsed.frag"
TR = HiCdataset("bla" + str(np.random.randint(100000000000)), genome=genomeFolder(working_genome),
maximumMoleculeLength=500, enzymeName=enzyme, tmpFolder="tmp",
inMemory=True) # remove inMemory if you don't have enough RAM
TR.parseInputData(dictLike=onename)
print onename
TR.save(ensure(finalname))
folder, fname = os.path.split(onename)
statSubFolder = os.path.join(stat_folder, folder)
TR.printMetadata(saveTo=ensure(os.path.join(statSubFolder, fname + ".stat")))
else:
# Create dataset at destination, parse on HDD, then no need to save.
TR = HiCdataset(ensure(onename + "_parsed.frag"),
genome=genomeFolder(working_genome), enzymeName=enzyme, tmpFolder="tmp",
maximumMoleculeLength=500, mode='w')
TR.parseInputData(dictLike=onename, enzymeToFillRsites=enzyme)
TR.printMetadata(saveTo=ensure(os.path.join(stat_folder, onename + ".stat")))
def refineDataset(filenames, create=True, delete=True, parseInMemory=True):
"""
Parameters
----------
filenames[0] is a list of filenames of incoming files
filenames[1] is a folder for outgoing file
filenames[2] is a working genome name, which is also the name of output directory
create : bool, optional
If True, parse each file.
If False, assume that files were already parsed
(e.g. if you are just playing around with filtering parameters)
delete : bool, optional
If True, delete parsed files after merging.
Man, these files may be huge... if you don't have a 10TB RAID, this may be useful.
parseInMemory : bool, optional
Perform parsing input files in memory.
"""
in_files = filenames[0]
out_file = filenames[1]
workingGenome = filenames[2]
if os.path.exists(workingGenome) == False:
try:
os.mkdir(workingGenome)
except:
print "Cannot create working directory"
exit()
if create == True: # if we need to parse the input files (.hdf5 from mapping).
for onename in in_files:
#Parsing individual files
if not os.path.exists(source(onename)):
raise StandardError("path not found: %s" % onename)
if parseInMemory == True:
#create dataset in memory, parse and then save to destination
TR = HiCdataset("bla", genome=genomeFolder(workingGenome),
maximumMoleculeLength=500, override=True,
inMemory=True) # remove inMemory if you don't have enough RAM
TR.parseInputData(dictLike=source(onename))
TR.save(onename + "_parsed.frag")
else:
#Create dataset at destination, parse on HDD, then no need to save.
TR = HiCdataset(onename + "_parsed.frag",
genome=genomeFolder(workingGenome),
maximumMoleculeLength=500, override=True)
TR.parseInputData(dictLike=source(onename))
"Merging files alltogether, applying filters"
TR = HiCdataset(out_file + "_merged.frag",
genome=genomeFolder(workingGenome),
override=True)
TR.merge([i + "_parsed.frag" for i in in_files])
#Merge in all parsed files from one experiment
if delete == True: # cleaning up parsed files
for delFile in [i + "_parsed.frag" for i in in_files]:
os.remove(delFile)
TR.flush()
"Now opening new dataset for refined data, and performing all the filtering "
TR = HiCdataset(out_file + "_refined.frag",
genome=genomeFolder(workingGenome),
override=True)
TR.load(out_file + "_merged.frag")
#----------------------------Set of filters applied -------------
TR.filterRsiteStart(offset=5)
TR.filterDuplicates()
#TR.save(out_file+".dat")
TR.filterLarge()
TR.filterExtreme(cutH=0.005, cutL=0)
#------------------------End set of filters applied----------
else:
#If merging & filters has already been done, just load files
TR = HiCdataset(out_file + "_working.frag",
override=True, genome=genomeFolder(workingGenome))
TR.load(out_file + "_refined.frag")
print "----->Building Raw heatmap at two resolutions"
TR.printStats()
TR.saveHeatmap(out_file + "-200k.hm", 200000)
TR.saveHeatmap(out_file + "-500k.hm", 500000)
TR.saveHeatmap(out_file + "-1M.hm", 1000000)
TR.saveHeatmap(out_file + "-2M.hm", 2000000)
print "----->Building RB heatmap"
TR = HiCdataset(out_file + "_breaks.frag", genome=genomeFolder(
workingGenome), override=True)
TR.load(out_file + "_refined.frag")
TR.maskFilter((TR.dists1 > TR.maximumMoleculeLength) + (TR.dists2 >
TR.maximumMoleculeLength) * TR.DS)
TR.printStats()
TR.saveHeatmap(out_file + "-200k-breaks.hm", 200000)
TR.saveHeatmap(out_file + "-500k-breaks.hm", 500000)
TR.saveHeatmap(out_file + "-1M-breaks.hm", 1000000)
TR.saveHeatmap(out_file + "-2M-breaks.hm", 2000000)
#Now running refineDataset for each experiment
for i in byExperiment:
refineDataset(i, create=True, delete=True)
#Now merging different experiments alltogether
experiments = set([(i[0], i[2]) for i in newExperimentNames])
for experiment in experiments:
workingGenome = experiment[1]
myExperimentNames = [i[1] + "_refined.frag" for i in newExperimentNames if i[0] == experiment[0]]
assert len(myExperimentNames) > 0
if len(myExperimentNames) > 1:
TR = HiCdataset(os.path.join(workingGenome, "%s-all_refined.frag" %
experiment[0]), genome=genomeFolder(workingGenome))
TR.merge(myExperimentNames)
TR.saveHeatmap(os.path.join(
workingGenome, "%s-all-100k.hm" % experiment[0]), 100000)
TR.saveHeatmap(os.path.join(
workingGenome, "%s-all-200k.hm" % experiment[0]), 200000)
TR.saveHeatmap(os.path.join(
workingGenome, "%s-all-500k.hm" % experiment[0]), 500000)
TR.saveHeatmap(os.path.join(
workingGenome, "%s-all-1M.hm" % experiment[0]), 1000000)
#map(refine_paper,
# [((source("SRR027961"),
# source("SRR027960")), os.path.join(workingGenome, "GM-NcoI-%s" % workingGenome ),"NcoI"),
chrms1 = np.random.randint(0,22,N)
chrms2 = chrms1.copy()
mask = np.random.random(N) < 0.5
chrms2[mask] = np.random.randint(0,22,mask.sum())
pos1 = np.array(np.array((0.1 + 0.8 * np.random.random(N)) * mygenome.chrmLens[chrms1]), dtype=int)
offset1 = np.exp(3 + np.random.random(N) * (np.log(1000000) - 3)) * (2 * (np.random.random(N)>0.5) - 1 )
pos2 = np.array(pos1 + offset1, dtype=int)
strands1 = np.random.random(N) > 0.5
strands2 = np.random.random(N) > 0.5
mydict = {"chrms1":chrms1, "chrms2":chrms2,"cuts1":pos1,"cuts2":pos2,"strands1":strands1,"strands2":strands2}
TR = HiCdataset("bla", genome=mygenome, enzymeName="MboI",maximumMoleculeLength=500, inMemory=True)
print "\nTesting loading new data without rsite information "
TR.parseInputData(dictLike=mydict,
enzymeToFillRsites="MboI")
TR.filterLarge(cutlarge=50000, cutsmall=100)
sc = TR.plotScaling()
print sc
plt.title("Scaling should be 1/x")
plt.plot(*sc)
plt.xscale("log")
plt.yscale("log")
plt.show()
def refine_paper(filename, create=True):
"""filename[0] is a list of filenames of incoming files
filename[1] is a folder for outgoing file"""
if create == True:
for onename in filename[0]:
#Parsing individual files
if not os.path.exists(onename):
raise StandardError("path not found: %s" % onename)
TR = HiCdataset("bla",
genome=genomeFolder,
enzymeName="HindIII",
maximumMoleculeLength=500,
inMemory=True)
print "\nTesting loading new data without rsite information "
TR.parseInputData(dictLike=onename, enzymeToFillRsites="HindIII")
#assert len(TR.DS) == 856143
#assert len(TR.ufragments) == 634572
TR.save(onename + "_parsed.frag")
#Merging files alltogether, applying filters
TR = HiCdataset(filename[1] + "_merged.frag",
enzymeName="HindIII",
genome=genomeFolder,
mode="w")
TR.merge([i + "_parsed.frag" for i in filename[0]])
TR = HiCdataset("refined",
genome=genomeFolder,
enzymeName="HindIII",
mode="w",
inMemory=True)
print "\nTesting chunking during all tests"
TR.chunksize = 30000
#because we do many operations, we disable autoFlush here
TR.load(filename[1] + "_merged.frag")
print "\nTesting Rsite filter"
TR.filterRsiteStart(offset=5)
#assert len(TR.DS) == 832110
print "\nTesting duplicate filter"
TR.filterDuplicates(chunkSize=30000)
#assert len(TR.DS) == 830275
print "\nTesting small/large and extreme fragment filter"
TR.filterLarge()
#assert len(TR.DS) == 825442
TR.filterExtreme(cutH=0.005, cutL=0)
TR.writeFilteringStats()
#assert len(TR.DS) == 803845
#-------------------------------------------
TR.printMetadata(saveTo="metadata")
import cPickle
stop = False
mdata = cPickle.load(open("sampleMetadata"))
for i in sorted(mdata.keys()):
if TR.metadata[i] != mdata[i]:
print "Key {0} is not consistent: should be {1}, is {2}".format(
i, mdata[i], TR.metadata[i])
stop = True
if stop == True:
print("""------------_ERROR_--------------
Inconsistent metadata: see above
----------------------------------------""")
raise ValueError("Inconsistent Metadata")
print "Testing allxall and by-chromosome heatmap counting diagonal twice"
print "----> saving allxall heatmap"
TR.saveHeatmap(filename[1] + "-1M.hm", 1000000, countDiagonalReads="twice")
a = h5dict(filename[1] + "-1M.hm")
st, end = TR.genome.chrmStartsBinCont[1], TR.genome.chrmEndsBinCont[1]
st2, end2 = TR.genome.chrmStartsBinCont[2], TR.genome.chrmEndsBinCont[2]
chrom1 = a["heatmap"][st:end, st:end]
chrom12 = a["heatmap"][st:end, st2:end2]
setExceptionHook()
print "----> saving by chromosome heatmap"
TR.saveByChromosomeHeatmap(filename[1] + "-1M.hm",
resolution=1000000,
includeTrans=True,
countDiagonalReads="twice")
b = h5dict(filename[1] + "-1M.hm")["1 1"]
bb = h5dict(filename[1] + "-1M.hm")["1 2"]
assert (b - chrom1).sum() == 0
print "Cis heatmap consistent"
assert (bb - chrom12).sum() == 0
print 'Trans heatmap consistent'
print a["heatmap"][::10, ::10].sum()
#assert a["heatmap"][::10, ::10].sum() == 21800
print "Heatmap sum correct\n"
#---------------------------------
print "Testing allxall and by-chromosome heatmap counting diagonal once"
TR.saveHeatmap(filename[1] + "-1M.hm", 1000000, countDiagonalReads="once")
Ta = h5dict(filename[1] + "-1M.hm")
st, end = TR.genome.chrmStartsBinCont[1], TR.genome.chrmEndsBinCont[1]
st2, end2 = TR.genome.chrmStartsBinCont[2], TR.genome.chrmEndsBinCont[2]
chrom1 = Ta["heatmap"][st:end, st:end]
chrom12 = Ta["heatmap"][st:end, st2:end2]
setExceptionHook()
print "----> saving by chromosome heatmap"
TR.saveByChromosomeHeatmap(filename[1] + "-1M-byChr.hm",
resolution=1000000,
includeTrans=True,
countDiagonalReads="once")
TR.saveHiResHeatmapWithOverlaps(filename[1] + "-1M-highRes.hm",
resolution=50000,
countDiagonalReads="twice")
TR.saveSuperHighResMapWithOverlaps(filename[1] + "-5k-SuperHighRes.hm",
resolution=5000,
chromosomes=[14],
countDiagonalReads="twice")
Tb = h5dict(filename[1] + "-1M-byChr.hm")["1 1"]
Tbb = h5dict(filename[1] + "-1M-byChr.hm")["1 2"]
assert ((Tb - chrom1) == 0).all()
assert ((Tbb - chrom12) == 0).all()
assert ((Tb + np.diag(np.diag(Tb))) == b).all()
print "Diagonal counting methods are consistent\n"
newchrom1 = chrom1.copy()
for i in xrange(len(newchrom1)):
newchrom1[i, i] = 2 * newchrom1[i, i]
Tb = h5dict(filename[1] + "-1M-highRes.hm")["1 1"]
assert np.abs(Tb.sum() - newchrom1.sum()) < 1
assert np.sum(np.abs(coarsegrain(Tb, 20, True) - newchrom1)) < 500
#------------------------------
print "Testing updateGenome method"
from mirnylib.genome import Genome
removeChromIDs = np.array([0, 1, 1, 1, 1] + [0] * 17 + [1] + [0])
#print ((removeChromIDs[TR.chrms1] == 1) + (removeChromIDs[TR.chrms2] == 1) ).sum()
t = ((removeChromIDs[TR.chrms1] == 1) *
(removeChromIDs[TR.chrms2] == 1)).sum() + (
(removeChromIDs[TR.chrms1] == 1) * (TR.chrms2 == -1)).sum()
newGenome = Genome(genomePath=genomeFolder,
readChrms=["2", "3", "4", "5", "X"])
TR.updateGenome(newGenome)
assert TR.N == t
a = h5dict(filename[1] + "-1M.hm")["heatmap"]
"""
from hiclib.fragmentHiC import HiCdataset
import os
from mirnylib import genome
genomeDb = genome.Genome('../data/caul',
chrmFileTemplate="%s.fa",
readChrms=[])
for expName in os.listdir("caul"):
TR = HiCdataset(
"bla",
genome=genomeDb,
inMemory=True,
) # inMemory, as files are probably small (less than hundreds mililon reads)
TR.parseInputData("caul/" + expName,
removeSS=True) # We discard SS in our pipeline now
TR.printMetadata()
TR.filterRsiteStart(
offset=5
) # We still do this filter to avoid strange "dangling end-like" molecules
TR.filterDuplicates()
#TR.save(out_file+".dat")
TR.filterLarge(
cutlarge=300000, cutsmall=100
) #Don't filter any large fragments. This was relevant for eucaryotes with
#their megabase-long stretches of repetitive or unmappable regions
#TR.filterExtreme(cutH=0.0025, cutL=0) #ALl fragments in Caulobacter seemed to behave normally
pass
#Now merging different experiments alltogether
#note that the first column is not here, as it is a replica
experiments = set([(i[0], i[2], i[3]) for i in combinedExperimentNames])
print(experiments)
for experiment in experiments:
workingGenome = experiment[1]
myExperimentNames = [i[1] + "_refined.frag" for i in combinedExperimentNames if (i[0], i[2], i[3]) == (experiment[0], experiment[1],experiment[2])]
assert len(myExperimentNames) > 0
if len(myExperimentNames) > 0:
#If we have more than one experiment (replica) for the same data, we can combine.
TR = HiCdataset(os.path.join(workingGenome, "%s-all-%s_refined.frag" %
(experiment[0],experiment[2])), genome=getGenome(workingGenome),
enzymeName = experiment[2],tmpFolder = "tmp",dictToStoreIDs="h5dict")
statSaveName = os.path.join("statistics", workingGenome, "%s-all-%s_refined.stat" % (experiment[0], experiment[2]))
TR.merge(myExperimentNames)
TR.printMetadata(saveTo=statSaveName)
for res in wholeGenomeResolutionsKb:
TR.saveHeatmap(os.path.join(workingGenome, "%s-all-%s-{0}k.hm" % (experiment[0], experiment[2])).format(res), res*1000)
for res in byChromosomeResolutionsKb:
TR.saveByChromosomeHeatmap(os.path.join(workingGenome, "%s-all-%s-{0}k.byChr" % (experiment[0], experiment[2])).format(res), res*1000)
for res in HiResWithOverlapResolutionsKb:
TR.saveHiResHeatmapWithOverlaps(os.path.join(workingGenome, "%s-all-%s-{0}k_HighRes.byChr" % (experiment[0], experiment[2])).format(res), res*1000)
for res in SuperHiResWithOverlapResolutionsKb:
TR.saveSuperHighResMapWithOverlaps(os.path.join(workingGenome, "%s-all-%s-{0}k_SuperHighRes.byChr" % (experiment[0], experiment[2])).format(res), res*1000)
def plotFigure2c():
TR = HiCdataset()
TR.load("GM-all.refined")
hm = TR.buildHeatmap(1, 1, 1000000, False, False)
TR.calculateWeights()
TR.weights = np.ones(
len(TR.weights), float
) # if you want to correct just by fragment density, not by length dependence
hm2 = TR.buildHeatmap(1, 1, 1000000, False, weights=True)
hm2[np.isnan(hm2)] = 0
mask = np.sum(hm, axis=0) > 0
"""p1-6 are 6 lines to be plotted, below is plotting only"""
p1 = np.sum(hm, axis=0)[mask]
p3 = np.sum(correct(hm), axis=0)[mask]
p5 = np.sum(ultracorrect(hm, 40), axis=0)[mask]
p4 = np.sum(correct(hm2), axis=0)[mask]
p2 = np.sum(hm2, axis=0)[mask]
p6 = np.sum(ultracorrect(hm2, 40), axis=0)[mask]
matplotlib.rcParams['font.sans-serif'] = 'Arial'
dashstyle = (3, 3)
plt.figure(figsize=(4, 4))
ax = plt.subplot(2, 1, 1)
plt.xlim((0, 80))
plt.ylim((0, 2))
plt.ylabel("Total coverage", fontsize=8)
line21 = plt.plot(p1 / p1.mean(), "-", linewidth=1, color="#e5a826")[0]
line22 = plt.plot(p3 / p3.mean(), "--", linewidth=1, color="#e5a826")[0]
line22.set_dashes(dashstyle)
line23 = plt.plot(p5 / p5.mean(), linewidth=1, color="grey")[0]
for xlabel_i in ax.get_xticklabels():
xlabel_i.set_fontsize(8)
for xlabel_i in ax.get_yticklabels():
xlabel_i.set_fontsize(8)
legend = plt.legend(
[line21, line22, line23],
["Raw data", "Single correction", "Iterative correction"],
prop={"size": 6},
loc=1,
handlelength=2)
legend.draw_frame(False)
removeAxes(shift=0, ax=ax)
for i in ax.spines.values():
i.set_color('none')
ax.axhline(linewidth=1, color='black')
ax.axvline(linewidth=1, color='black')
ax2 = plt.subplot(2, 1, 2, sharex=ax)
plt.xlim((0, 80))
plt.ylim((0, 2))
plt.xlabel("Position on chom 1 (MB)", fontsize=8)
plt.ylabel("Total coverage", fontsize=8)
line1 = plt.plot(p4 / p4.mean(), "--", color="#9b3811", linewidth=1)[0]
line1.set_dashes(dashstyle)
line2 = plt.plot(p2 / p2.mean(), "-", color="#9b3811", linewidth=1)[0]
line3 = plt.plot(p6 / p6.mean(), linewidth=1, color="grey")[0]
for xlabel_i in ax2.get_xticklabels():
xlabel_i.set_fontsize(8)
for xlabel_i in ax2.get_yticklabels():
xlabel_i.set_fontsize(8)
legend = plt.legend(
[line2, line1, line3],
["HindIII corrected", "Single correction", "Iterative correction"],
prop={"size": 6},
loc=1,
handlelength=2)
legend.draw_frame(False)
removeAxes(shift=0, ax=ax2)
plotting.niceShow()
chrms1 = np.random.randint(0,22,N)
chrms2 = chrms1.copy()
mask = np.random.random(N) < 0.5
chrms2[mask] = np.random.randint(0,22,mask.sum())
pos1 = np.array(np.array((0.1 + 0.8 * np.random.random(N)) * mygenome.chrmLens[chrms1]), dtype=int)
offset1 = np.exp(3 + np.random.random(N) * (np.log(1000000) - 3)) * (2 * (np.random.random(N)>0.5) - 1 )
pos2 = np.array(pos1 + offset1, dtype=int)
strands1 = np.random.random(N) > 0.5
strands2 = np.random.random(N) > 0.5
mydict = {"chrms1":chrms1, "chrms2":chrms2,"cuts1":pos1,"cuts2":pos2,"strands1":strands1,"strands2":strands2}
TR = HiCdataset("bla", genome=mygenome, enzymeName="MboI",maximumMoleculeLength=500, inMemory=True)
print("\nTesting loading new data without rsite information ")
TR.parseInputData(dictLike=mydict,
enzymeToFillRsites="MboI")
TR.filterLarge(cutlarge=50000, cutsmall=100)
sc = TR.plotScaling()
g = mygenome
print(sc)
plt.title("Scaling should be 1/x")
plt.plot(*sc)
plt.xscale("log")
plt.yscale("log")
def refineDataset(filenames, create=True, delete=False, parseInMemory=True):
"""
Parameters
----------
filenames[0] is a list of filenames of incoming files
filenames[1] is a folder for outgoing file
filenames[2] is a working genome, that is output directory
filenames[3] is an enzyme for a given experiment
create : bool, optional
If True, parse each file.
If False, assume that files were already parsed
(e.g. if you are just playing around with filtering parameters)
delete : bool, optional
If True, delete parsed files after merging.
Man, these files may be huge... if you don't have a 10TB RAID, this may be useful.
parseInMemory : bool, optional
Perform parsing input files in memory.
"""
in_files = filenames[0]
out_file = filenames[1]
statFolder = os.path.join("statistics", out_file)
workingGenome = filenames[2]
enzyme = filenames[3]
if create == True: # if we need to parse the input files (.hdf5 from mapping).
def parse_onename(onename):
np.random.seed()
#Parsing individual files
if parseInMemory == True:
finalname = onename + "_parsed.frag"
#if not os.path.exists(finalname):
if True:
#create dataset in memory, parse and then save to destination
TR = HiCdataset(
"bla" + str(np.random.randint(100000000000)),
genome=getGenome(workingGenome),
maximumMoleculeLength=500,
enzymeName=enzyme,
tmpFolder="tmp",
inMemory=True
) # remove inMemory if you don't have enough RAM
TR.parseInputData(dictLike=onename)
folder = os.path.split(onename)[0]
print(onename)
TR.save(ensure(finalname))
folder, fname = os.path.split(onename)
statSubFolder = os.path.join(statFolder, folder)
TR.printMetadata(saveTo=ensure(
os.path.join(statSubFolder, fname + ".stat")))
else:
print("skipping parsed: ", onename)
else:
#Create dataset at destination, parse on HDD, then no need to save.
TR = HiCdataset(ensure(onename + "_parsed.frag"),
genome=getGenome(workingGenome),
enzymeName=enzyme,
tmpFolder="tmp",
maximumMoleculeLength=500,
mode='w')
TR.parseInputData(dictLike=onename, enzymeToFillRsites=enzyme)
TR.printMetadata(
saveTo=ensure(os.path.join(statFolder, onename + ".stat")))
list(map(parse_onename, in_files))
"Merging files alltogether, applying filters"
TR = HiCdataset(ensure(out_file + "_merged.frag"),
genome=getGenome(workingGenome),
enzymeName=enzyme,
tmpFolder="tmp",
dictToStoreIDs="h5dict",
mode="w")
TR.merge([i + "_parsed.frag" for i in in_files])
#Merge in all parsed files from one experiment
if delete == True: # cleaning up parsed files
for delFile in [i + "_parsed.frag" for i in in_files]:
os.remove(delFile)
"Now opening new dataset for refined data, and performing all the filtering "
TR = HiCdataset(out_file + "_refined.frag",
enzymeName=enzyme,
genome=getGenome(workingGenome),
tmpFolder="tmp",
dictToStoreIDs="h5dict",
mode='w')
TR.load(out_file + "_merged.frag")
#----------------------------Set of filters applied -------------
TR.filterDuplicates()
#TR.save(out_file+".dat")
#TR.filterExtreme(cutH=0.0001, cutL=0)
#TR.filterRsiteStart()
#TR.filterLarge()
TR.writeFilteringStats()
TR.printMetadata(saveTo=statFolder + ".stat")
#------------------------End set of filters applied----------
else:
#If merging & filters has already been done, just load files
TR = HiCdataset(out_file + "_working.frag",
enzymeName=enzyme,
mode='w',
genome=getGenome(workingGenome))
TR.load(out_file + "_refined.frag")
TR.printMetadata(saveTo=statFolder + ".stat")
print("----->Building Raw heatmap at different resolutions")
TR.printStats()
for res in coolerResolutions:
TR.saveCooler(out_file + ".{0}.cool".format(res), res)
def doOne(inData):
coolResolutions = [
10000000, 5000000, 2000000, 1000000, 500000, 200000, 100000, 40000,
20000, 10000, 5000, 2000, 1000
]
i, j = inData
if i == "":
return
# if i not in ["total", "pronuc", "K562"]:
# continue
print(i)
gens = j["genome"]
if len(gens) == 0:
print("Genome not found")
return
genome = gens.values[0]
out_file = "{1}/{0}_combined".format(i, genome)
# if os.path.exists(out_file + "-10k_HighRes.byChr"):
# continue
mygen = "/home/magus/HiC2011/data/{0}".format(genome)
filenames = [
"{1}/{0}_refined.frag".format(s, genome) for s in j["filenames"].values
]
# assert False not in list(map(os.path.exists, filenames))
filenames = [i for i in filenames if os.path.exists(i)]
if len(filenames) == 0:
print("No filenames found!")
return
TR = HiCdataset("bla",
mygen,
"DpnII",
inMemory=True,
tmpFolder="/tmp",
dictToStoreIDs="dict")
TR.merge(filenames)
TR.setSimpleHighResHeatmap()
TR.writeFilteringStats()
TR.printMetadata(
saveTo="statistics/{1}/{0}_combined.frag".format(i, genome))
pickle.dump(
TR.metadata,
open("statistics/{1}/{0}_combined.pkl".format(i, genome), 'wb'))
TR.save("{1}/{0}_combined_refined.frag".format(i, genome))
for res in coolResolutions:
TR.saveCooler(out_file + ".{0}.cool".format(res), res)
from hiclib.fragmentHiC import HiCdataset
from mirnylib.systemutils import fmap, setExceptionHook
from mirnylib.genome import Genome
import os
#from defineGenome import getGenome
genomeName = "mm10"
genome_db = Genome("/mnt/storage/home/vsfishman/HiC/fasta/" + genomeName,
readChrms=["#", "X", "Y"])
data_folder = "/mnt/storage/home/vsfishman/HiC/data/mESC/mapped-mm10/mm10/"
fdataset_fname = "mESC-all-HindIII_refined.frag"
setExceptionHook()
print "Loading HiCdataset"
TR = HiCdataset(data_folder + fdataset_fname,
enzymeName="HindIII",
mode='r',
genome=genome_db)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "1000k.hm", 1000000)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "40k.hm", 40000)
print "Saving heatmap"
TR.saveHeatmap(data_folder + fdataset_fname + "25k.hm",
25000,
useFragmentOverlap=True)
#print "Saving Hi-Res heatmap"
#TR.saveHiResHeatmapWithOverlaps(data_folder + fdataset_fname + "10k_hiRes.hm", 10000)
def doSupplementaryCoveragePlot():
TR = HiCdataset()
TR.load("GM-all.refined")
s1 = TR.fragmentSum(strands=1)
TR.saveFragments()
TR.maskFilter(TR.dists1 > 500)
TR.originalFragments()
s2 = TR.fragmentSum(strands=1)
resolution = 1000000
def coverage(s1, s2, TR):
genome = Genome()
genome.createMapping(resolution)
label = genome.chromosomeStarts[TR.ufragments / TR.fragIDmult - 1] + (
TR.ufragments % TR.fragIDmult) / resolution
counts = np.bincount(label, weights=s1)
counts2 = np.bincount(label, weights=s2)
data = cPickle.load(open("GC1M", 'rb'))
eigenvector = np.zeros(genome.chromosomeEnds[-1], float)
inds = np.argsort(counts)
mask = inds[int(0.02 * len(inds)):]
for chrom in range(1, 24):
eigenvector[genome.chromosomeStarts[chrom - 1]:genome.
chromosomeStarts[chrom - 1] +
len(data[chrom - 1])] = data[chrom - 1]
eigenvector[eigenvector < 35] = 35
plt.scatter(counts[mask],
counts2[mask],
c=eigenvector[mask],
s=6,
linewidth=0)
print stats.spearmanr(counts[mask], counts2[mask])
plt.xlabel("Coverage from all reads")
plt.xticks([0, 5000, 10000, 15000])
plt.ylabel("Coverage from RBs")
b = plt.colorbar()
b.ax.set_xlabel("GC content")
plt.subplot(121)
plt.title("HinIII")
coverage(s1, s2, TR)
TR = HiCdataset()
TR.load("GM-NcoI.refined")
s1 = TR.fragmentSum(strands=1)
TR.saveFragments()
TR.maskFilter(TR.dists1 > 500)
TR.originalFragments()
s2 = TR.fragmentSum(strands=1)
resolution = 1000000
plt.subplot(122)
plt.title("NcoI")
coverage(s1, s2, TR)
plt.show()
#Now running refineDataset for each experiment
for i in byExperiment:
print i
refineDataset(i, create=True, delete=True)
#Now merging different experiments alltogether
#note that the first column is not here, as it is a replica
experiments = set([(i[0], i[2], i[3]) for i in combinedExperimentNames])
print experiments
for experiment in experiments:
workingGenome = experiment[1]
myExperimentNames = [i[1] + "_refined.frag" for i in combinedExperimentNames if (i[0], i[2], i[3]) == (experiment[0], experiment[1],experiment[2])]
assert len(myExperimentNames) > 0
if len(myExperimentNames) > 1:
#If we have more than one experiment (replica) for the same data, we can combine.
TR = HiCdataset(os.path.join(workingGenome, "%s-all-%s_refined.frag" %
(experiment[0],experiment[2])), genome=genomeFolder(workingGenome))
statSaveName = os.path.join("statistics", workingGenome, "%s-all-%s_refined.stat" % (experiment[0], experiment[2]))
TR.merge(myExperimentNames)
TR.printMetadata(saveTo=statSaveName)
for res in wholeGenomeResolutionsKb:
TR.saveHeatmap(os.path.join(workingGenome, "%s-all-%s-{0}k.hm" % (experiment[0], experiment[2])).format(res), res*1000)
for res in byChromosomeResolutionsKb:
TR.saveByChromosomeHeatmap(os.path.join(workingGenome, "%s-all-%s-{0}k.byChr" % (experiment[0], experiment[2])).format(res), res*1000)
for res in HiResWithOverlapResolutionsKb:
TR.saveHiResHeatmapWithOverlaps(os.path.join(workingGenome, "%s-all-%s-{0}k_HighRes.byChr" % (experiment[0], experiment[2])).format(res), res*1000)
def parse_onename(onename):
np.random.seed()
#Parsing individual files
if parseInMemory == True:
finalname = onename + "_parsed.frag"
#if not os.path.exists(finalname):
if True:
#create dataset in memory, parse and then save to destination
TR = HiCdataset(
"bla" + str(np.random.randint(100000000000)),
genome=getGenome(workingGenome),
maximumMoleculeLength=500,
enzymeName=enzyme,
tmpFolder="tmp",
inMemory=True
) # remove inMemory if you don't have enough RAM
TR.parseInputData(dictLike=onename)
folder = os.path.split(onename)[0]
print(onename)
TR.save(ensure(finalname))
folder, fname = os.path.split(onename)
statSubFolder = os.path.join(statFolder, folder)
TR.printMetadata(saveTo=ensure(
os.path.join(statSubFolder, fname + ".stat")))
else:
print("skipping parsed: ", onename)
else:
#Create dataset at destination, parse on HDD, then no need to save.
TR = HiCdataset(ensure(onename + "_parsed.frag"),
genome=getGenome(workingGenome),
enzymeName=enzyme,
tmpFolder="tmp",
maximumMoleculeLength=500,
mode='w')
TR.parseInputData(dictLike=onename, enzymeToFillRsites=enzyme)
TR.printMetadata(
saveTo=ensure(os.path.join(statFolder, onename + ".stat")))
from mirnylib.systemutils import fmap, setExceptionHook
from mirnylib.genome import Genome
import os
#from defineGenome import getGenome
genomeName = "mm10"
genome_db = Genome("/mnt/storage/home/vsfishman/HiC/fasta/" + genomeName,
readChrms=["#", "X", "Y"])
data_folder = "/mnt/storage/home/vsfishman/HiC/data/mESC/mapped-mm10/mm10/"
fdataset_fname = "mESC-all-HindIII_refined.frag"
setExceptionHook()
print "Loading HiCdataset"
TR = HiCdataset(data_folder + fdataset_fname,
enzymeName="HindIII",
mode='r',
genome=genome_db)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "1000k.hm", 1000000)
#print "Saving heatmap"
#TR.saveHeatmap(data_folder + fdataset_fname + "40k.hm", 40000)
print "Saving heatmap"
TR.saveHeatmap(data_folder + fdataset_fname + "15k.hm",
15000,
useFragmentOverlap=True)
print "Saving Hi-Res heatmap"
TR.saveHiResHeatmapWithOverlaps(data_folder + fdataset_fname + "10k_hiRes.hm",
10000)
def doSupplementaryCoveragePlot():
TR = HiCdataset()
TR.load("GM-all.refined")
s1 = TR.fragmentSum(strands=1)
TR.saveFragments()
TR.maskFilter(TR.dists1 > 500)
TR.originalFragments()
s2 = TR.fragmentSum(strands=1)
resolution = 1000000
def coverage(s1, s2, TR):
genome = Genome()
genome.createMapping(resolution)
label = genome.chromosomeStarts[TR.ufragments / TR.fragIDmult -
1] + (TR.ufragments % TR.fragIDmult) / resolution
counts = np.bincount(label, weights=s1)
counts2 = np.bincount(label, weights=s2)
data = cPickle.load(open("GC1M", 'rb'))
eigenvector = np.zeros(genome.chromosomeEnds[-1], float)
inds = np.argsort(counts)
mask = inds[int(0.02 * len(inds)):]
for chrom in range(1, 24):
eigenvector[genome.chromosomeStarts[chrom - 1]:genome.chromosomeStarts[chrom - 1] + len(data[chrom - 1])] = data[chrom - 1]
eigenvector[eigenvector < 35] = 35
plt.scatter(counts[mask], counts2[mask], c=eigenvector[
mask], s=6, linewidth=0)
print stats.spearmanr(counts[mask], counts2[mask])
plt.xlabel("Coverage from all reads")
plt.xticks([0, 5000, 10000, 15000])
plt.ylabel("Coverage from RBs")
b = plt.colorbar()
b.ax.set_xlabel("GC content")
plt.subplot(121)
plt.title("HinIII")
coverage(s1, s2, TR)
TR = HiCdataset()
TR.load("GM-NcoI.refined")
s1 = TR.fragmentSum(strands=1)
TR.saveFragments()
TR.maskFilter(TR.dists1 > 500)
TR.originalFragments()
s2 = TR.fragmentSum(strands=1)
resolution = 1000000
plt.subplot(122)
plt.title("NcoI")
coverage(s1, s2, TR)
plt.show()
"""
This scripts is a rip-off of a large mergeDatasets script with certain adjustments.
Follow comments along the text.
"""
from hiclib.fragmentHiC import HiCdataset
import os
from mirnylib import genome
genomeDb = genome.Genome('../data/caul', chrmFileTemplate="%s.fa", readChrms=[])
for expName in os.listdir("caul"):
TR = HiCdataset("bla", genome=genomeDb, inMemory=True,) # inMemory, as files are probably small (less than hundreds mililon reads)
TR.parseInputData("caul/" + expName, removeSS=True) # We discard SS in our pipeline now
TR.printMetadata()
TR.filterRsiteStart(offset=5) # We still do this filter to avoid strange "dangling end-like" molecules
TR.filterDuplicates()
#TR.save(out_file+".dat")
TR.filterLarge(cutlarge=300000, cutsmall=100) #Don't filter any large fragments. This was relevant for eucaryotes with
#their megabase-long stretches of repetitive or unmappable regions
#TR.filterExtreme(cutH=0.0025, cutL=0) #ALl fragments in Caulobacter seemed to behave normally
TR.writeFilteringStats()
TR.printMetadata(saveTo=statFolder + ".stat")
TR.save("data/" + expName + "_refined.frag") #Saving filtered dataset
#Below, saving all datasets at different resolutions.
#Also, using new feature - fragment overlaps - which assins reads to all bins the fragment crosses.
TR.saveHeatmap("data/" + expName + "-5k_overlap.hm", 5000, useFragmentOverlap=True)
def refineDataset(filenames, create=True, delete=True, parseInMemory=True):
"""
Parameters
----------
filenames[0] is a list of filenames of incoming files
filenames[1] is a folder for outgoing file
filenames[2] is a working genome, that is output directory
filenames[3] is an enzyme for a given experiment
create : bool, optional
If True, parse each file.
If False, assume that files were already parsed
(e.g. if you are just playing around with filtering parameters)
delete : bool, optional
If True, delete parsed files after merging.
Man, these files may be huge... if you don't have a 10TB RAID, this may be useful.
parseInMemory : bool, optional
Perform parsing input files in memory.
"""
in_files = filenames[0]
out_file = filenames[1]
statFolder = os.path.join("statistics", out_file)
workingGenome = filenames[2]
enzyme = filenames[3]
if create == True: # if we need to parse the input files (.hdf5 from mapping).
for onename in in_files:
#Parsing individual files
if parseInMemory == True:
#create dataset in memory, parse and then save to destination
TR = HiCdataset("bla", genome=genomeFolder(workingGenome),
maximumMoleculeLength=500,
inMemory=True) # remove inMemory if you don't have enough RAM
TR.parseInputData(dictLike=onename, enzymeToFillRsites=enzyme)
folder = os.path.split(onename)[0]
print onename
TR.save(ensure(onename + "_parsed.frag"))
folder, fname = os.path.split(onename)
statSubFolder = os.path.join(statFolder, folder)
TR.printMetadata(saveTo=ensure(os.path.join(statSubFolder, fname + ".stat")))
else:
#Create dataset at destination, parse on HDD, then no need to save.
TR = HiCdataset(ensure(onename + "_parsed.frag"),
genome=genomeFolder(workingGenome),
maximumMoleculeLength=500, mode='w')
TR.parseInputData(dictLike=onename, enzymeToFillRsites=enzyme)
TR.printMetadata(saveTo=ensure(os.path.join(statFolder, onename + ".stat")))
"Merging files alltogether, applying filters"
TR = HiCdataset(ensure(out_file + "_merged.frag"),
genome=genomeFolder(workingGenome),
mode="w")
TR.merge([i + "_parsed.frag" for i in in_files])
#Merge in all parsed files from one experiment
if delete == True: # cleaning up parsed files
for delFile in [i + "_parsed.frag" for i in in_files]:
os.remove(delFile)
"Now opening new dataset for refined data, and performing all the filtering "
TR = HiCdataset(out_file + "_refined.frag",
genome=genomeFolder(workingGenome),
mode='w')
TR.load(out_file + "_merged.frag")
#----------------------------Set of filters applied -------------
TR.filterRsiteStart(offset=5)
TR.filterDuplicates()
#TR.save(out_file+".dat")
TR.filterLarge()
TR.filterExtreme(cutH=0.005, cutL=0)
TR.writeFilteringStats()
TR.printMetadata(saveTo=statFolder + ".stat")
#------------------------End set of filters applied----------
else:
#If merging & filters has already been done, just load files
TR = HiCdataset(out_file + "_working.frag",
mode='w', genome=genomeFolder(workingGenome))
TR.load(out_file + "_refined.frag")
TR.printMetadata(saveTo=statFolder + ".stat")
print "----->Building Raw heatmap at different resolutions"
TR.printStats()
for res in wholeGenomeResolutionsKb:
TR.saveHeatmap(out_file + "-{0}k.hm".format(res), res*1000)
for res in byChromosomeResolutionsKb:
TR.saveByChromosomeHeatmap(out_file + "-{0}k.byChr".format(res), res*1000)
for res in HiResWithOverlapResolutionsKb:
TR.saveHiResHeatmapWithOverlaps(out_file + "-{0}k_HighRes.byChr".format(res), res*1000)
def heatmapFromHotFragments(dataset="../../../mouse/data/combined/"\
"mouse1_merged.frag",
workingFile="../../../tcc/working/workingMouse.frag",
cacheFile="../../../tcc/working/workingMouseFiltered.frag",
genomeFolder="../../../data/mm9",
label=""):
mirnylib.systemutils.setExceptionHook()
if not os.path.exists(cacheFile):
FH = HiCdataset(workingFile, genomeFolder)
FH.load(dataset)
FH.filterRsiteStart(offset=5)
FH.filterDuplicates()
#TR.save(filename[1]+".dat")
FH.filterLarge()
FH.maskFilter(FH.DS)
FH.save(cacheFile)
FH = HiCdataset(workingFile, genomeFolder)
FH.load(cacheFile)
fs = FH.fragmentSum()
p996, p998 = numpy.percentile(fs, [99.6, 99.8])
frag96 = FH.ufragments[fs > p996]
frag98 = FH.ufragments[(fs > p998)]
FH.maskFilter(arrayInArray(
FH.fragids1, frag96) + arrayInArray(FH.fragids2, frag96))
hm98100 = FH.buildAllHeatmap(5000000)
FH.maskFilter(arrayInArray(
FH.fragids1, frag98) + arrayInArray(FH.fragids2, frag98))
hm99100 = FH.buildAllHeatmap(5000000)
plt.subplot(121)
plt.imshow(numpy.log(hm99100 + 1), interpolation="nearest")
plt.colorbar()
plt.title("log # counts for top .2 % of fragments, " + label)
plt.subplot(122)
plt.imshow(numpy.log(hm98100 - hm99100 + 1), interpolation="nearest")
plt.title("log # counts for second top .2% (.996 - .998), " + label)
plt.colorbar()
plt.show()
def refine_paper(filename, create=True):
"""filename[0] is a list of filenames of incoming files
filename[1] is a folder for outgoing file"""
if create == True:
for onename in filename[0]:
#Parsing individual files
if not os.path.exists(onename):
raise StandardError("path not found: %s" % onename)
TR = HiCdataset("bla", genome=genomeFolder, enzymeName="HindIII",maximumMoleculeLength=500, inMemory=True)
print "\nTesting loading new data without rsite information "
TR.parseInputData(dictLike=onename,
enzymeToFillRsites="HindIII")
#assert len(TR.DS) == 856143
#assert len(TR.ufragments) == 634572
TR.save(onename + "_parsed.frag")
#Merging files alltogether, applying filters
TR = HiCdataset(filename[1] + "_merged.frag",enzymeName = "HindIII",
genome=genomeFolder, mode="w")
TR.merge([i + "_parsed.frag" for i in filename[0]])
TR = HiCdataset("refined", genome=genomeFolder,enzymeName = "HindIII",
mode="w", inMemory=True)
print "\nTesting chunking during all tests"
TR.chunksize = 30000
#because we do many operations, we disable autoFlush here
TR.load(filename[1] + "_merged.frag")
print "\nTesting Rsite filter"
TR.filterRsiteStart(offset=5)
#assert len(TR.DS) == 832110
print "\nTesting duplicate filter"
TR.filterDuplicates(chunkSize = 30000)
#assert len(TR.DS) == 830275
print "\nTesting small/large and extreme fragment filter"
TR.filterLarge()
#assert len(TR.DS) == 825442
TR.filterExtreme(cutH=0.005, cutL=0)
TR.writeFilteringStats()
#assert len(TR.DS) == 803845
#-------------------------------------------
TR.printMetadata(saveTo="metadata")
import cPickle
stop = False
mdata = cPickle.load(open("sampleMetadata"))
for i in sorted(mdata.keys()):
if TR.metadata[i] != mdata[i]:
print "Key {0} is not consistent: should be {1}, is {2}".format(i, mdata[i], TR.metadata[i])
stop = True
if stop == True:
print ("""------------_ERROR_--------------
Inconsistent metadata: see above
----------------------------------------""")
raise ValueError("Inconsistent Metadata")
print "Testing allxall and by-chromosome heatmap counting diagonal twice"
print "----> saving allxall heatmap"
TR.saveHeatmap(filename[1] + "-1M.hm", 1000000,
countDiagonalReads="twice")
a = h5dict(filename[1] + "-1M.hm")
st, end = TR.genome.chrmStartsBinCont[1], TR.genome.chrmEndsBinCont[1]
st2, end2 = TR.genome.chrmStartsBinCont[2], TR.genome.chrmEndsBinCont[2]
chrom1 = a["heatmap"][st:end, st:end]
chrom12 = a["heatmap"][st:end, st2:end2]
setExceptionHook()
print "----> saving by chromosome heatmap"
TR.saveByChromosomeHeatmap(
filename[1] + "-1M.hm", resolution=1000000, includeTrans=True,
countDiagonalReads="twice")
b = h5dict(filename[1] + "-1M.hm")["1 1"]
bb = h5dict(filename[1] + "-1M.hm")["1 2"]
assert (b - chrom1).sum() == 0
print "Cis heatmap consistent"
assert (bb - chrom12).sum() == 0
print 'Trans heatmap consistent'
print a["heatmap"][::10, ::10].sum()
#assert a["heatmap"][::10, ::10].sum() == 21800
print "Heatmap sum correct\n"
#---------------------------------
print "Testing allxall and by-chromosome heatmap counting diagonal once"
TR.saveHeatmap(filename[1] + "-1M.hm", 1000000,
countDiagonalReads="once")
Ta = h5dict(filename[1] + "-1M.hm")
st, end = TR.genome.chrmStartsBinCont[1], TR.genome.chrmEndsBinCont[1]
st2, end2 = TR.genome.chrmStartsBinCont[2], TR.genome.chrmEndsBinCont[2]
chrom1 = Ta["heatmap"][st:end, st:end]
chrom12 = Ta["heatmap"][st:end, st2:end2]
setExceptionHook()
print "----> saving by chromosome heatmap"
TR.saveByChromosomeHeatmap(
filename[1] + "-1M-byChr.hm", resolution=1000000, includeTrans=True,
countDiagonalReads="once")
TR.saveHiResHeatmapWithOverlaps(filename[1]+"-1M-highRes.hm", resolution=50000, countDiagonalReads="twice")
TR.saveSuperHighResMapWithOverlaps(filename[1]+"-5k-SuperHighRes.hm", resolution=5000,chromosomes = [14], countDiagonalReads="twice")
Tb = h5dict(filename[1] + "-1M-byChr.hm")["1 1"]
Tbb = h5dict(filename[1] + "-1M-byChr.hm")["1 2"]
assert ((Tb - chrom1) == 0).all()
assert ((Tbb - chrom12) == 0).all()
assert ((Tb + np.diag(np.diag(Tb))) == b).all()
print "Diagonal counting methods are consistent\n"
newchrom1 = chrom1.copy()
for i in xrange(len(newchrom1)):
newchrom1[i,i] = 2 * newchrom1[i,i]
Tb = h5dict(filename[1] + "-1M-highRes.hm")["1 1"]
assert np.abs(Tb.sum() - newchrom1.sum()) < 1
assert np.sum(np.abs(coarsegrain(Tb,20,True) - newchrom1)) < 500
#------------------------------
print "Testing updateGenome method"
from mirnylib.genome import Genome
removeChromIDs = np.array([0, 1, 1, 1, 1] + [0] * 17 + [1] + [0])
#print ((removeChromIDs[TR.chrms1] == 1) + (removeChromIDs[TR.chrms2] == 1) ).sum()
t = ((removeChromIDs[TR.chrms1] == 1) * (removeChromIDs[TR.chrms2] == 1)).sum() + ((removeChromIDs[TR.chrms1] == 1) * (TR.chrms2 == -1)).sum()
newGenome = Genome(genomePath=genomeFolder, readChrms=["2",
"3", "4", "5", "X"])
TR.updateGenome(newGenome)
assert TR.N == t
a = h5dict(filename[1] + "-1M.hm")["heatmap"]
def plotCisToTransHotFragments(dataset="../../../mouse/data/combined/"\
"mouse1_merged.frag",
workingFile="../../../tcc/working/workingMouse.frag",
cacheFile="../../../tcc/working/workingMouseFiltered.frag",
genomeFolder="../../../data/mm9", label=None):
mirnylib.systemutils.setExceptionHook()
if not os.path.exists(cacheFile):
print "caching parsed data"
FH = HiCdataset(workingFile, genomeFolder)
FH.load(dataset)
FH.filterRsiteStart(offset=5)
FH.filterDuplicates()
#TR.save(filename[1]+".dat")
FH.filterLarge()
FH.maskFilter(FH.DS)
FH.save(cacheFile)
FH = HiCdataset(workingFile, genomeFolder)
FH.load(cacheFile)
fs = FH.fragmentSum()
FH.saveFragments()
FH.maskFilter(FH.chrms1 == FH.chrms2)
FH.originalFragments()
fsCis = FH.fragmentSum()
args = numpy.argsort(fs)
fsSort = 1. * fs[args]
fsCisSort = 1. * fsCis[args]
cisToTrans = fsCisSort / fsSort
p1, p2, p3 = numpy.percentile(fsSort, [99, 99.5, 99.9])
bins = mirnylib.numutils.logbins(1, fsSort.max(), 1.08)
counts = numpy.histogram(fsSort, bins)
values = numpy.histogram(fsSort, bins, weights=cisToTrans)
plt.plot(0.5 * (values[1][:-1] + values[1][1:]), values[0] /
counts[0], '.', label=label)
for linep in p1, p2, p3:
plt.vlines(linep, 0, 1)
plt.xlabel("Counts per fragment")
plt.ylabel("Cis-to-trans ratio")
plt.title("Vertical lines are at 99%,99.5% and 99.9% reads per fragment")
niceShow()
