def test_call():
tmp = os.path.join(pybedtools.get_tempdir(), 'test.output')
from pybedtools.helpers import call_bedtools, BEDToolsError
assert_raises(BEDToolsError, call_bedtools, *(['intersectBe'], tmp))
a = pybedtools.example_bedtool('a.bed')
# momentarily redirect stderr to file so the error message doesn't spew all
# over the place when testing
orig_stderr = sys.stderr
sys.stderr = open(a._tmp(), 'w')
#assert_raises(BEDToolsError, a.intersect, a=a.fn, b=a.fn, z=True)
sys.stderr = orig_stderr
pybedtools.set_bedtools_path('nonexistent')
a = pybedtools.example_bedtool('a.bed')
assert_raises(OSError, a.intersect, a)
pybedtools.set_bedtools_path()
assert a.intersect(a,u=True) == a
def test_call():
tmp = os.path.join(pybedtools.get_tempdir(), "test.output")
from pybedtools.helpers import call_bedtools, BEDToolsError
with pytest.raises(BEDToolsError):
call_bedtools(*(["intersectBe"], tmp))
a = pybedtools.example_bedtool("a.bed")
# momentarily redirect stderr to file so the error message doesn't spew all
# over the place when testing
orig_stderr = sys.stderr
sys.stderr = open(a._tmp(), "w")
sys.stderr = orig_stderr
pybedtools.set_bedtools_path("nonexistent")
a = pybedtools.example_bedtool("a.bed")
with pytest.raises(NotImplementedError):
a.intersect(a)
pybedtools.set_bedtools_path()
a = pybedtools.example_bedtool("a.bed")
assert a.intersect(a, u=True) == a
def __init__(self, arg, log, *array, **dicts):
self.arg = arg
self.log = log
self.array = array
self.dicts = dicts
self.arg.scriptdir = os.path.dirname(os.path.realpath(__file__))
self.arg.datadir = self.arg.scriptdir + '/../Data/'
self.arg.Bam = '%s/%s'%(self.arg.indir, self.arg.bamdir)
self.arg.Fetch = '%s/%s'%(self.arg.outdir, self.arg.fetchdir)
self.arg.Search = '%s/%s'%(self.arg.outdir, self.arg.searchdir)
self.arg.Merge = '%s/%s'%(self.arg.outdir, self.arg.mergedir)
self.arg.Region = '%s/%s'%(self.arg.outdir, self.arg.regiondir)
self.arg.Cheak = '%s/%s'%(self.arg.outdir, self.arg.checkdir)
self.arg.CNV = '%s/%s'%(self.arg.outdir, self.arg.cnvdir)
if self.arg.commands == 'Auto':
self.arg.Pipe = self.arg.pipeline
else:
self.arg.Pipe = self.arg.commands
CORES = multiprocessing.cpu_count()*0.8 if multiprocessing.cpu_count() >8 else 8
os.environ['NUMEXPR_MAX_THREADS'] = '1000' #str(int(CORES))
os.environ['PATH'] += ':' + self.arg.bedtools
importlib.reload(bt)
bt.set_bedtools_path(self.arg.bedtools)
def gcbias_lite(coveragefile, bedfilename, reference, fileout, graphtitle=None, executiongranted=None, status=None, bedTools=False):
"""************************************************************************************************************************************************************
Task: draws coverage as a function of gc content. IMPROVED VERSION of gcbias that avoids the use of bedtools (pybedtools)
Input:
coveragefile: string containing the full path of the bam.coverage file to analyze. This file has been built according to 1-base format
bedfilename: target file -> assumes original-standard bed file
reference: fasta file with reference genome
fileout: string containing the full path of the bmp file where the restulting figure will be saved.
bedTools: whether pybedtools are used instead of the own method
Output: a png file will be created named "fileout" where a graph that compares gc content and mean coverage will be saved.
************************************************************************************************************************************************************"""
if(executiongranted<>None):
executiongranted.acquire()
pid = str(os.getpid())
# print 'Processing '+coveragefile
# print 'Results will be written at '+fileout
coverage = region_coverage(coveragefile) # Calculate mean coverage per region
## fdw=file('regionCoverage.txt','w')
## for element in sorted(coverage.keys()):
## fdw.write(str(element)+'\n')
## fdw.close()
if(len(coverage)>1):
if not bedTools: # Own method
# print 'Own method'
chromosomes={}
allKeys=coverage.keys()
for currentKey in allKeys:
chromosomes[currentKey[0]]=1 # Stores all chromosomes to be examined (the ones contained in the target file)
# Load BED file -> since coverage information is in 1-base format, BED format must be transformed to 1-base
bed=bed_file.bed_file(bedfilename)
sortedBed=bed.my_sort_bed() # Sort bed avoiding bedtools
nonOverlappingBed=sortedBed.non_overlapping_exons(1) # Base 1!!! # This generates a BED file in base 1 (Non-standard BED)
finalBed=nonOverlappingBed.my_sort_bed() # BED file in base 1 (Non-standard BED)
finalBed.load_custom(-1) # Load chromosome and positions in base 1....(finalBed is in base 1 -> Non-standard BED)
#Load FASTA file
fastaFile=file(reference,'r')
storeSequence=False
wholeChromosome=''
currentChromosome=''
gccontent={}
for line in fastaFile: # Read each line of the fasta file
if line.startswith('>'): # New chromosome starts -> reading a new line until another '>' is found
# print 'Processing ' +line+'\n'
if storeSequence: # a chromosome has been read run gc bias
currentGCcontent=measureGCbias(wholeChromosome,currentChromosome,finalBed)
gccontent.update(currentGCcontent) # Update dictionary
storeSequence=False
currentChromosome=re.split(' +',line)[0] # Format: >1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
currentChromosome=currentChromosome.split('>')[1].strip() # Chromosome string
if(currentChromosome in chromosomes): # If current chromosome read in the FASTA file is in the list of chromosomes in the BED file
storeSequence=True
wholeChromosome='' # To store whole sequence for the current chromosome
elif (not re.search('>',line) and storeSequence):
wholeChromosome=wholeChromosome+line.rstrip() # Remove '\n' from current line and concatenates to wholeChromosome
if(storeSequence): # For the last chromosome
currentGCcontent=measureGCbias(wholeChromosome,currentChromosome,finalBed)
gccontent.update(currentGCcontent) # Update dictionary
fastaFile.close()
region_ids=[]
region_ids = coverage.keys()
if(len(gccontent)==0):
print 'ERROR: G+C content values can not be calculated. Probably the provided reference file '+reference+' does not match with '
print ' the target file '+bedfilename+'. That is, sequences of regions in the target file are probably not included within the'
print ' reference file.'
sys.exit(1)
else:
print 'Calculating nt content by means of pybedtools...'
bed=bed_file.bed_file(bedfilename)
sortedBed=bed.my_sort_bed() # Sort bed avoiding bedtools
nonOverlappingBed=sortedBed.non_overlapping_exons(1) # base one!!!
finalBed=nonOverlappingBed.my_sort_bed() # BED file in base 1
bedfd = pybedtools.BedTool(finalBed.filename)
bedfd=bedfd.remove_invalid() # Remove negative coordinates or features with length=0, which do not work with bedtools
pybedtools._bedtools_installed = True
pybedtools.set_bedtools_path(BEDTOOLSPATH)
ntcontent = bedfd.nucleotide_content(reference)
# Each entry in ntcontent is parsed to extract the gc content of each exon
gccontent = {}
for entry in ntcontent:
gccontent[(entry.fields[0], string.atoi(entry.fields[1]), string.atoi(entry.fields[2]))] = string.atof(entry.fields[-8])*100
print ' Done.'
# gccontent keys in dictionary: chromosome, exon init, exon end
region_ids=[]
for currentKey in coverage.keys(): # Pybedtools does not work with regions with zero length -> remove them (there are a few of them)
if currentKey[1]!=currentKey[2]:
region_ids.append(currentKey)
##
## fdw=file('gcContent.txt','w')
## for element in sorted(gccontent.keys()):
## fdw.write(str(element)+'\n')
## fdw.close()
##
#region_ids = gccontent.keys()
coveragearray = numpy.array([coverage[id] for id in region_ids])
gccontentarray = numpy.array([gccontent[id] for id in region_ids]) # Values in [0,1]
# fig = pyplot.figure(figsize=(6,6))
# ax = fig.add_subplot(111)
#
# ax.hist(gccontentarray,bins=100)
# fig.suptitle('Dsitribution of GC content regardless of coverage value')
# ax.set_ylabel('Frequency')
# ax.set_xlabel('GC content')
# ax.set_xlim(0, 100)
# fig.savefig('distribution.png')
xmin = gccontentarray.min()
xmax = gccontentarray.max() # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
ymin = coveragearray.min()
ymax = coveragearray.max()
# Perform a kernel density estimator on the results
X, Y = mgrid[xmin:xmax:100j, ymin:ymax:100j]
positions = c_[X.ravel(), Y.ravel()]
values = c_[gccontentarray, coveragearray]
kernel = stats.kde.gaussian_kde(values.T)
Z = reshape(kernel(positions.T).T, X.T.shape)
fig = pyplot.figure(figsize=(6,6))
ax = fig.add_subplot(111)
sc=ax.imshow(rot90(Z),cmap=cm.gist_earth_r,extent=[xmin, 100, ymin, ymax], aspect="auto") # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
cbar=fig.colorbar(sc,ticks=[numpy.min(Z),numpy.max(Z)])
cbar.ax.set_yticklabels(['Low','High'])
cbar.set_label('Density')
ax.set_xlabel('GC content (%)')
ax.set_ylabel('Mean coverage')
if(len(graphtitle)>25):
ax.set_title(graphtitle[:25]+'...')
else:
ax.set_title(graphtitle)
fig.savefig(fileout)
matplotlib.pyplot.close(fig)
if(status<>None):
meanvalue = gccontentarray.mean()
status.value = (meanvalue>=45 and meanvalue<=55)
else:
print 'WARNING: only one region found in the bed file. Skipping GC bias calculation.'
if(executiongranted<>None):
executiongranted.release()
def gcbias(filelist, fileoutlist, bedfilelist):
"""************************************************************************************************************************************************************
Task: draws coverage as a function of gc content
Input:
filelist: list of strings, each containing the full path of the bam file to analyze.
fileoutlist: list of strings, each containing the full path of the png file where the corresponding figure will be saved.
bedfilelist:
Output: a bmp file will be created named "fileout" where a graph that compares gc content and mean coverage will be saved.
************************************************************************************************************************************************************"""
pid = str(os.getpid())
numpy.random.seed(1)
ntotal_positions = []
bamlist = []
# Process each file and store counting results
for filename in filelist:
# Check whether index already exists for the bam file, needed for pysam use
if(not os.path.isfile(filename+'.bai')):
print 'Creating index for '+filename
pysam.index(filename)
print ' Done.'
bamlist.append(bam_file.bam_file(filename))
sizes = numpy.array([bam.nreads() for bam in bamlist])
minsize = sizes.min()
print 'The smaller bam is '+filelist[sizes.argmin()]+' and contains '+str(minsize)+' reads.'
# Process each file and store counting results
for i,bamfile in enumerate(bamlist):
print 'Processing '+bamfile.filename
print 'Results will be written at '+fileoutlist[i]
# Check whether normalization should be run
if(normalize): normalizedbam = bamfile.normalize(minsize)
else: normalizedbam = bamfile
coveragefile = TMP+'/'+pid+'.coverage'
print 'Calculating coverage per position...'
run(BEDTOOLSPATH+'coverageBed -d -abam '+normalizedbam.filename+' -b '+bedfilelist[i]+' > '+coveragefile)
coverage = region_coverage(coveragefile)
print 'Calculating nt content...'
bedfd = pybedtools.BedTool(bedfilelist[i])
pybedtools._bedtools_installed = True
pybedtools.set_bedtools_path(BEDTOOLSPATH)
ntcontent = bedfd.nucleotide_content(REF)
# Each entry in ntcontent is parsed to extract the gc content of each exon
gccontent = {}
for entry in ntcontent:
gccontent[(entry.fields[0], string.atoi(entry.fields[1]), string.atoi(entry.fields[2]))] = string.atof(entry.fields[-8])*100
print ' Done.'
fig = pyplot.figure(figsize=(13,6))
ax = fig.add_subplot(111)
region_ids = coverage.keys()
coveragearray = numpy.array([coverage[id] for id in region_ids])
gccontentarray = numpy.array([gccontent[id] for id in region_ids]) # Values in [0,1]
xmin = gccontentarray.min()
xmax = gccontentarray.max() # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
ymin = coveragearray.min()
ymax = coveragearray.max()
# Perform a kernel density estimator on the results
X, Y = mgrid[xmin:xmax:100j, ymin:ymax:100j]
positions = c_[X.ravel(), Y.ravel()]
values = c_[gccontentarray, coveragearray]
kernel = stats.kde.gaussian_kde(values.T)
Z = reshape(kernel(positions.T).T, X.T.shape)
fig = pyplot.figure(figsize=(6,6))
ax = fig.add_subplot(111)
sc=ax.imshow(rot90(Z),cmap=cm.gist_earth_r,extent=[xmin, 100, ymin, ymax], aspect="auto") # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
cbar=fig.colorbar(sc,ticks=[numpy.min(Z),numpy.max(Z)])
cbar.ax.set_yticklabels(['Low','High'])
cbar.set_label('Density')
ax.set_xlabel('GC content (%)')
ax.set_ylabel('Mean coverage')
fig.savefig(fileoutlist[i])
matplotlib.pyplot.close(fig)
print '>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finished <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<'
def gcbias_lite(coveragefile,
bedfilename,
reference,
fileout,
graphtitle=None,
executiongranted=None,
status=None,
bedTools=False):
"""************************************************************************************************************************************************************
Task: draws coverage as a function of gc content. IMPROVED VERSION of gcbias that avoids the use of bedtools (pybedtools)
Input:
coveragefile: string containing the full path of the bam.coverage file to analyze. This file has been built according to 1-base format
bedfilename: target file -> assumes original-standard bed file
reference: fasta file with reference genome
fileout: string containing the full path of the bmp file where the restulting figure will be saved.
bedTools: whether pybedtools are used instead of the own method
Output: a png file will be created named "fileout" where a graph that compares gc content and mean coverage will be saved.
************************************************************************************************************************************************************"""
if (executiongranted <> None):
executiongranted.acquire()
pid = str(os.getpid())
# print 'Processing '+coveragefile
# print 'Results will be written at '+fileout
coverage = region_coverage(
coveragefile) # Calculate mean coverage per region
## fdw=file('regionCoverage.txt','w')
## for element in sorted(coverage.keys()):
## fdw.write(str(element)+'\n')
## fdw.close()
if (len(coverage) > 1):
if not bedTools: # Own method
# print 'Own method'
chromosomes = {}
allKeys = coverage.keys()
for currentKey in allKeys:
chromosomes[currentKey[
0]] = 1 # Stores all chromosomes to be examined (the ones contained in the target file)
# Load BED file -> since coverage information is in 1-base format, BED format must be transformed to 1-base
bed = bed_file.bed_file(bedfilename)
sortedBed = bed.my_sort_bed() # Sort bed avoiding bedtools
nonOverlappingBed = sortedBed.non_overlapping_exons(
1
) # Base 1!!! # This generates a BED file in base 1 (Non-standard BED)
finalBed = nonOverlappingBed.my_sort_bed(
) # BED file in base 1 (Non-standard BED)
finalBed.load_custom(
-1
) # Load chromosome and positions in base 1....(finalBed is in base 1 -> Non-standard BED)
#Load FASTA file
fastaFile = file(reference, 'r')
storeSequence = False
wholeChromosome = ''
currentChromosome = ''
gccontent = {}
for line in fastaFile: # Read each line of the fasta file
if line.startswith(
'>'
): # New chromosome starts -> reading a new line until another '>' is found
# print 'Processing ' +line+'\n'
if storeSequence: # a chromosome has been read run gc bias
currentGCcontent = measureGCbias(
wholeChromosome, currentChromosome, finalBed)
gccontent.update(currentGCcontent) # Update dictionary
storeSequence = False
currentChromosome = re.split(
' +', line
)[0] # Format: >1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
currentChromosome = currentChromosome.split(
'>')[1].strip() # Chromosome string
if (
currentChromosome in chromosomes
): # If current chromosome read in the FASTA file is in the list of chromosomes in the BED file
storeSequence = True
wholeChromosome = '' # To store whole sequence for the current chromosome
elif (not re.search('>', line) and storeSequence):
wholeChromosome = wholeChromosome + line.rstrip(
) # Remove '\n' from current line and concatenates to wholeChromosome
if (storeSequence): # For the last chromosome
currentGCcontent = measureGCbias(wholeChromosome,
currentChromosome, finalBed)
gccontent.update(currentGCcontent) # Update dictionary
fastaFile.close()
region_ids = []
region_ids = coverage.keys()
if (len(gccontent) == 0):
print 'ERROR: G+C content values can not be calculated. Probably the provided reference file ' + reference + ' does not match with '
print ' the target file ' + bedfilename + '. That is, sequences of regions in the target file are probably not included within the'
print ' reference file.'
sys.exit(1)
else:
print 'Calculating nt content by means of pybedtools...'
bed = bed_file.bed_file(bedfilename)
sortedBed = bed.my_sort_bed() # Sort bed avoiding bedtools
nonOverlappingBed = sortedBed.non_overlapping_exons(
1) # base one!!!
finalBed = nonOverlappingBed.my_sort_bed() # BED file in base 1
bedfd = pybedtools.BedTool(finalBed.filename)
bedfd = bedfd.remove_invalid(
) # Remove negative coordinates or features with length=0, which do not work with bedtools
pybedtools._bedtools_installed = True
pybedtools.set_bedtools_path(BEDTOOLSPATH)
ntcontent = bedfd.nucleotide_content(reference)
# Each entry in ntcontent is parsed to extract the gc content of each exon
gccontent = {}
for entry in ntcontent:
gccontent[(entry.fields[0], string.atoi(entry.fields[1]),
string.atoi(entry.fields[2]))] = string.atof(
entry.fields[-8]) * 100
print ' Done.'
# gccontent keys in dictionary: chromosome, exon init, exon end
region_ids = []
for currentKey in coverage.keys(
): # Pybedtools does not work with regions with zero length -> remove them (there are a few of them)
if currentKey[1] != currentKey[2]:
region_ids.append(currentKey)
##
## fdw=file('gcContent.txt','w')
## for element in sorted(gccontent.keys()):
## fdw.write(str(element)+'\n')
## fdw.close()
##
#region_ids = gccontent.keys()
coveragearray = numpy.array([coverage[id] for id in region_ids])
gccontentarray = numpy.array([gccontent[id]
for id in region_ids]) # Values in [0,1]
# fig = pyplot.figure(figsize=(6,6))
# ax = fig.add_subplot(111)
#
# ax.hist(gccontentarray,bins=100)
# fig.suptitle('Dsitribution of GC content regardless of coverage value')
# ax.set_ylabel('Frequency')
# ax.set_xlabel('GC content')
# ax.set_xlim(0, 100)
# fig.savefig('distribution.png')
xmin = gccontentarray.min()
xmax = gccontentarray.max(
) # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
ymin = coveragearray.min()
ymax = coveragearray.max()
# Perform a kernel density estimator on the results
X, Y = mgrid[xmin:xmax:100j, ymin:ymax:100j]
positions = c_[X.ravel(), Y.ravel()]
values = c_[gccontentarray, coveragearray]
kernel = stats.kde.gaussian_kde(values.T)
Z = reshape(kernel(positions.T).T, X.T.shape)
fig = pyplot.figure(figsize=(6, 6))
ax = fig.add_subplot(111)
sc = ax.imshow(
rot90(Z),
cmap=cm.gist_earth_r,
extent=[xmin, 100, ymin, ymax],
aspect="auto"
) # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
cbar = fig.colorbar(sc, ticks=[numpy.min(Z), numpy.max(Z)])
cbar.ax.set_yticklabels(['Low', 'High'])
cbar.set_label('Density')
ax.set_xlabel('GC content (%)')
ax.set_ylabel('Mean coverage')
if (len(graphtitle) > 25):
ax.set_title(graphtitle[:25] + '...')
else:
ax.set_title(graphtitle)
fig.savefig(fileout)
matplotlib.pyplot.close(fig)
if (status <> None):
meanvalue = gccontentarray.mean()
status.value = (meanvalue >= 45 and meanvalue <= 55)
else:
print 'WARNING: only one region found in the bed file. Skipping GC bias calculation.'
if (executiongranted <> None):
executiongranted.release()
def gcbias(filelist, fileoutlist, bedfilelist):
"""************************************************************************************************************************************************************
Task: draws coverage as a function of gc content
Input:
filelist: list of strings, each containing the full path of the bam file to analyze.
fileoutlist: list of strings, each containing the full path of the png file where the corresponding figure will be saved.
bedfilelist:
Output: a bmp file will be created named "fileout" where a graph that compares gc content and mean coverage will be saved.
************************************************************************************************************************************************************"""
pid = str(os.getpid())
numpy.random.seed(1)
ntotal_positions = []
bamlist = []
# Process each file and store counting results
for filename in filelist:
# Check whether index already exists for the bam file, needed for pysam use
if (not os.path.isfile(filename + '.bai')):
print 'Creating index for ' + filename
pysam.index(filename)
print ' Done.'
bamlist.append(bam_file.bam_file(filename))
sizes = numpy.array([bam.nreads() for bam in bamlist])
minsize = sizes.min()
print 'The smaller bam is ' + filelist[
sizes.argmin()] + ' and contains ' + str(minsize) + ' reads.'
# Process each file and store counting results
for i, bamfile in enumerate(bamlist):
print 'Processing ' + bamfile.filename
print 'Results will be written at ' + fileoutlist[i]
# Check whether normalization should be run
if (normalize): normalizedbam = bamfile.normalize(minsize)
else: normalizedbam = bamfile
coveragefile = TMP + '/' + pid + '.coverage'
print 'Calculating coverage per position...'
run(BEDTOOLSPATH + 'coverageBed -d -abam ' + normalizedbam.filename +
' -b ' + bedfilelist[i] + ' > ' + coveragefile)
coverage = region_coverage(coveragefile)
print 'Calculating nt content...'
bedfd = pybedtools.BedTool(bedfilelist[i])
pybedtools._bedtools_installed = True
pybedtools.set_bedtools_path(BEDTOOLSPATH)
ntcontent = bedfd.nucleotide_content(REF)
# Each entry in ntcontent is parsed to extract the gc content of each exon
gccontent = {}
for entry in ntcontent:
gccontent[(entry.fields[0], string.atoi(
entry.fields[1]), string.atoi(
entry.fields[2]))] = string.atof(entry.fields[-8]) * 100
print ' Done.'
fig = pyplot.figure(figsize=(13, 6))
ax = fig.add_subplot(111)
region_ids = coverage.keys()
coveragearray = numpy.array([coverage[id] for id in region_ids])
gccontentarray = numpy.array([gccontent[id]
for id in region_ids]) # Values in [0,1]
xmin = gccontentarray.min()
xmax = gccontentarray.max(
) # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
ymin = coveragearray.min()
ymax = coveragearray.max()
# Perform a kernel density estimator on the results
X, Y = mgrid[xmin:xmax:100j, ymin:ymax:100j]
positions = c_[X.ravel(), Y.ravel()]
values = c_[gccontentarray, coveragearray]
kernel = stats.kde.gaussian_kde(values.T)
Z = reshape(kernel(positions.T).T, X.T.shape)
fig = pyplot.figure(figsize=(6, 6))
ax = fig.add_subplot(111)
sc = ax.imshow(
rot90(Z),
cmap=cm.gist_earth_r,
extent=[xmin, 100, ymin, ymax],
aspect="auto"
) # Due to the imshow sentence, we need to rescale gccontent from [0,1] to [0,100]
cbar = fig.colorbar(sc, ticks=[numpy.min(Z), numpy.max(Z)])
cbar.ax.set_yticklabels(['Low', 'High'])
cbar.set_label('Density')
ax.set_xlabel('GC content (%)')
ax.set_ylabel('Mean coverage')
fig.savefig(fileoutlist[i])
matplotlib.pyplot.close(fig)
print '>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finished <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<'
from pybedtools import BedTool, set_bedtools_path
from nrlbio.pybedtools_extension import doublebed2dict, generate_overlaping_intervals
from nrlbio.interaction import Interaction
parser = argparse.ArgumentParser(description='converts bed-like file of chimeric reads into interactions. That is merging chimeras with intersecting regions');
parser.add_argument('path', metavar = 'N', nargs = '?', type = str, help = "Path to chimeras bed-like file");
parser.add_argument('-d', '--distance', nargs = '?', default = -12, type = int, help = "minimum overlap(negative number)/maximum distance(positive number) in nucleotides to merge intervals");
parser.add_argument('-n', '--name', nargs = '?', required = True, type = str, help = "name for interactions")
parser.add_argument('-oi', '--interactions', nargs = '?', required = True, type = str, help = "path to output interactions file")
parser.add_argument('-od', '--dictionary', nargs = '?', required = True, type = str, help = "path to output \"interaction to read id\" file")
parser.add_argument('--order', nargs = '?', default = False, const=True, type = int, help = "keeps order of left to right parts in interactions");
parser.add_argument('--bedtools', nargs = '?', default = '', type = str, help = "path to a bedtools binaries");
args = parser.parse_args();
set_bedtools_path(path=args.bedtools)
def intervals2interaction(intervals, distance, number, order=False):
if(order):
merged_regions = [[], []];
for interval in intervals:
merged_regions[int(interval.name.split("|")[-1])].append(interval)
else:
intervals.sort(key = attrgetter('chrom','strand','start'));
merged_regions = list(generate_overlaping_intervals(intervals, distance));
if(len(merged_regions)==2):
return Interaction.from_intervals("%s_%d" % (args.name, number), merged_regions)
from operator import itemgetter
from sequencing_tools.stats_tools import p_adjust
from sequencing_tools.fastq_tools import reverse_complement
from concensus_seq import concensus
from exon_coverage import ExonFilter
import pyBigWig as pbw
from tblout_parser import read_tbl
from sequencing_tools.bam_tools import get_strand
import pyximport
pyximport.install()
from junction_function import get_junction
import dask.dataframe as dd
import pyranges as pr
import io
from collections import Counter
set_bedtools_path('/stor/work/Lambowitz/cdw2854/src/miniconda3/bin')
set_tempdir('/stor/scratch/Lambowitz/cdw2854')
class GeneMapper():
def __init__(self):
self.HB_genes = '''chr11,5246694,5250625,HBB,-
chr11,5253908,5264887,HBD,-
chr11,5269309,5271089,HBG1,-
chr11,5274420,5526835,HBG2,-
chr11,5289575,5526882,HBE1,-
chr16,202686,204502,HBZ,+
chr16,203891,216767,HBM,+
chr14,50037702,50065882,RPS29,-
chr16,222875,223709,HBA2,+
