def count_reads(transcripts, bam_iter, number_of_counts=1):
""" Count the reads in a given transcript
:TODO rename
:TODO change to cython
Arguments
---------
transcripts : list
list of exons
bam_iter : pysam.BamFileIterator
gotton after pysam.BamFile.fetch() call
"""
# Convert this to Cython
out_counts = zeros(len(transcripts))
intron_lengths = []
read_vector = []
tree = Intersecter()
# Assume exons are position sorted
for ti, transcript in enumerate(transcripts):
ex_list = []
for j, i in enumerate(transcript):
tree.add_interval(
Interval(int(i[0]), int(i[1]), value={'anno': ti}))
if j != 0:
ex_list.append(transcript[j-1][1]\
- transcript[j][0])
intron_lengths.append(ex_list)
for read in bam_iter:
block_counter = zeros((len(transcripts), ))
intron_match = zeros((len(transcripts), ))
blocks = read.get_blocks()
junction_lengths = []
for i, j in enumerate(blocks):
if i != 0:
junction_lengths.append(blocks[i - 1][1] - j[0])
else:
pass
junction_lengths = set(junction_lengths)
for i, k in enumerate(blocks):
overlap = tree.find(k[0], k[1])
if len(overlap) == 0:
break
else:
for s in overlap:
if (k[0] >= s.start) and\
(k[1] <= s.end):
block_counter[s.value['anno']] += 1
for ij, il in enumerate(intron_lengths):
if set(junction_lengths).issubset(set(il)):
intron_match[ij] = 1
else:
pass
smatch = nrepeat(len(blocks), len(transcripts))
gg = logical_and(block_counter == smatch, intron_match)
read_vector.append(gg)
out_counts += gg
read_matrix = array(read_vector)
uniq_r = sum_(read_matrix, axis=1) == 1
#normalization_constant = [for i in transcripts]
return (out_counts)
def buildIntervalTree(exons):
'''Build interval tree from exon annotations.'''
tree = Intersecter()
for exon in exons:
tree.add_interval(Interval(exon.start, exon.end,
value={'cStart': exon.cStart,
'cEnd': exon.cEnd}))
return tree
def count_reads(transcripts, bam_iter, number_of_counts=1):
""" Count the reads in a given transcript
:TODO rename
:TODO change to cython
Arguments
---------
transcripts : list
list of exons
bam_iter : pysam.BamFileIterator
gotton after pysam.BamFile.fetch() call
"""
# Convert this to Cython
out_counts = zeros(len(transcripts))
intron_lengths = []
read_vector = []
tree = Intersecter()
# Assume exons are position sorted
for ti, transcript in enumerate(transcripts):
ex_list = []
for j, i in enumerate(transcript):
tree.add_interval(Interval(int(i[0]), int(i[1]),
value={'anno':ti}))
if j != 0:
ex_list.append(transcript[j-1][1]\
- transcript[j][0])
intron_lengths.append(ex_list)
for read in bam_iter:
block_counter = zeros((len(transcripts),))
intron_match = zeros((len(transcripts),))
blocks = read.get_blocks()
junction_lengths = []
for i,j in enumerate(blocks):
if i != 0:
junction_lengths.append(blocks[i - 1][1] - j[0])
else: pass
junction_lengths = set(junction_lengths)
for i, k in enumerate(blocks):
overlap = tree.find(k[0], k[1])
if len(overlap) == 0:
break
else:
for s in overlap:
if (k[0] >= s.start) and\
(k[1] <= s.end):
block_counter[s.value['anno']] += 1
for ij, il in enumerate(intron_lengths):
if set(junction_lengths).issubset(set(il)):
intron_match[ij] = 1
else: pass
smatch = nrepeat(len(blocks), len(transcripts))
gg = logical_and(block_counter == smatch, intron_match)
read_vector.append(gg)
out_counts += gg
read_matrix = array(read_vector)
uniq_r = sum_(read_matrix, axis=1) == 1
#normalization_constant = [for i in transcripts]
return(out_counts)
def init_intersecter(hits):
''' '''
intersecter = Intersecter()
for h in hits:
intersecter.add_interval(Interval(h[0], h[1]))
return intersecter
def init_intersecter(hits):
''' '''
intersecter = Intersecter()
for h in hits:
intersecter.add_interval(Interval(h[0], h[1]))
return intersecter
def load_restriction_fragment(in_file, minfragsize=None, maxfragsize=None, verbose=False):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
resFrag = {}
if verbose:
print "## Loading Restriction File Intervals '", in_file, "'..."
bed_handle = open(in_file)
nline = 0
nfilt = 0
for line in bed_handle:
nline +=1
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
print "Warning : wrong input format in line", nline,". Not a BED file !?"
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
fragl = abs(end - start)
name = name.strip()
## Discard fragments outside the size range
filt=False
if minfragsize != None and int(fragl) < int(minfragsize):
nfilt+=1
filt=True
elif maxfragsize != None and int(fragl) > int(maxfragsize):
nfilt+=1
filt=True
if chromosome in resFrag:
tree = resFrag[chromosome]
tree.add_interval(Interval(start, end, value={'name': name, 'filter': filt}))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end, value={'name': name, 'filter': filt}))
resFrag[chromosome] = tree
if nfilt > 0:
print "Warning : ", nfilt ,"fragment(s) outside of range and discarded. ", nline - nfilt, " remaining."
bed_handle.close()
return resFrag
def load_restriction_fragment(in_file, minfragsize=None, maxfragsize=None, verbose=False):
'''
This function cites the same function from Hi-C Pro (https://github.com/nservant/HiC-Pro/blob/master/scripts/mapped_2hic_fragments.py) by Nicolas Servant, Eric Viara
'''
'''
Function load_restriction_fragment cite the same function from Hi-C Pro (https://github.com/nservant/HiC-Pro/blob/master/scripts/mapped_2hic_fragments.py) by Nicolas Servant, Eric Viara
'''
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
resFrag = {}
if verbose:
print("## Loading Restriction File Intervals '" + in_file + "'...")
bed_handle = open(in_file)
nline = 0
for line in bed_handle:
nline +=1
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
print("Warning : wrong input format in line" + nline + ". Not a BED file !?")
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
midPoint = (start + end)/2
fragl = abs(end - start)
name = name.strip()
## Discard fragments outside the size range
if minfragsize != None and int(fragl) < int(minfragsize):
print("Warning : fragment "+ name + " [" + fragl + "] outside of range. Discarded")
continue
if maxfragsize != None and int(fragl) > int(maxfragsize):
print("Warning : fragment " + name + " [" + fragl + "] outside of range. Discarded")
continue
if chromosome in resFrag:
tree = resFrag[chromosome]
tree.add_interval(Interval(start, end, value={'name': name, 'midPoint': midPoint}))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end, value={'name': name, 'midPoint': midPoint}))
resFrag[chromosome] = tree
bed_handle.close()
return resFrag
def add_pvalues_to_peaks_frame_macs_bf(peaks_frame,experiment_peaks_frame,TTAA_frame,lam_win_size,pseudocounts = 0.2,macs_pvalue=True):
print "lab specific hohoho"
experiment_gnashy_dict = {}
experiment_dict_of_trees = {}
TTAA_frame_gbChr_dict = {}
TTAA_dict_of_trees = {}
list_of_l_names = [lam_win_size]
print "Making interval tree for experiment hops..."
for name,group in experiment_peaks_frame.groupby('Chr'):
experiment_gnashy_dict[name] = group
experiment_gnashy_dict[name].index = experiment_gnashy_dict[name]["Start"]
#initialize tree
experiment_dict_of_trees[name] = Intersecter()
#populate tree with position as interval
for idx, row in experiment_gnashy_dict[name].iterrows():
experiment_dict_of_trees[name].add_interval(Interval(int(idx),int(idx)+3))
print "Making interval tree for TTAAs..."
#make interval tree for TTAAs
for name,group in TTAA_frame.groupby('Chr'):
TTAA_frame_gbChr_dict[name] = group
TTAA_frame_gbChr_dict[name].index = TTAA_frame_gbChr_dict[name]["Start"]
#initialize tree
TTAA_dict_of_trees[name] = Intersecter()
#populate tree with position as interval
for idx, row in TTAA_frame_gbChr_dict[name].iterrows():
TTAA_dict_of_trees[name].add_interval(Interval(int(idx),int(idx+3)))
#go through cluster frame and compute pvalues
lambda_type_list =[]
lambda_list = []
pvalue_list = []
for idx,row in peaks_frame.iterrows():
#add number of background hops in cluster to frame
cluster_center = row["Center"]
#find lambda and compute significance of cluster
num_TTAAs = len(TTAA_dict_of_trees[row["Chr"]].find(row["Start"],row["End"]))
#compute lambda for window size
num_exp_hops_lam_win_size = len(experiment_dict_of_trees[row["Chr"]].find(cluster_center-(lam_win_size/2 - 1),cluster_center+lam_win_size/2))
num_TTAAs_lam_win_size = len(TTAA_dict_of_trees[row["Chr"]].find(cluster_center-(lam_win_size/2 - 1),cluster_center+lam_win_size/2))
lambda_win_size = float(num_exp_hops_lam_win_size)/(max(num_TTAAs_lam_win_size,1))
lambda_f = lambda_win_size
lambda_type_list.append(lam_win_size)
lambda_list.append(lambda_f)
#compute pvalue and record it
pvalue = 1-scistat.poisson.cdf((row["Experiment Hops"]+pseudocounts),lambda_f*max(num_TTAAs,1)+pseudocounts)
pvalue_list.append(pvalue)
#make frame from all of the lists
peaks_frame["Lambda Type"] = lambda_type_list
peaks_frame["Lambda"] = lambda_list
peaks_frame["Poisson pvalue"] = pvalue_list
return peaks_frame
def load_restriction_fragment(in_file, minfragsize=None, maxfragsize=None, verbose=False):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
resFrag = {}
if verbose:
print "## Loading Restriction File Intervals '", in_file, "'..."
bed_handle = open(in_file)
nline = 0
for line in bed_handle:
nline +=1
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
print "Warning : wrong input format in line", nline,". Not a BED file !?"
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
fragl = abs(end - start)
name = name.strip()
## Discard fragments outside the size range
if minfragsize != None and int(fragl) < int(minfragsize):
print "Warning : fragment ", name, " [", fragl, "] outside of range. Discarded"
continue
if maxfragsize != None and int(fragl) > int(maxfragsize):
print "Warning : fragment ", name, " [", fragl,"] outside of range. Discarded"
continue
if chromosome in resFrag.keys():
tree = resFrag[chromosome]
tree.add_interval(Interval(start, end, value={'name': name}))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end, value={'name': name}))
resFrag[chromosome] = tree
bed_handle.close()
return resFrag
def find_overlap_dataframes(query, hits):
'''
find overlap between sorted query and hits regions
:param query: [pd.DataFrame] query peaks
:param hits: [pd.DataFrame] hits regions
:return: flags [array]
'''
query_idx, hits_labs = [], []
tree_hash = {chrom: Intersecter() for chrom in hits.chrom.unique()}
null_res = [
tree_hash[chrom].add_interval(Interval(start, end))
for chrom, start, end in hits.values
]
for idx, line in enumerate(query.values):
chrom, start, end = line[0:3]
overlaps = tree_hash[chrom].find(start, end)
if not overlaps: continue
for ovp in overlaps:
hits_labs.append(chrom + ':' + str(ovp.start) + '-' + str(ovp.end))
query_idx.append(idx)
tmp_labels = hits.chrom + ':' + hits.start.astype(
str) + '-' + hits.end.astype(str)
hit_indexs = tmp_labels[tmp_labels.isin(hits_labs)].index.values
return np.array(query_idx), hit_indexs
def load_bed(read_length, path, flanking):
"""
parse bed file and ignore overlapping regions
:param path: BED file path
:param flanking: Integer to add to each target's start and end
:return: dictionary of targets where keys are chrom,start,end
"""
targets = {}
unique_targets = []
bed = BedTool(path)
for record in bed:
chrom, start, end = record[0], int(record[1]), int(record[2])
start -= flanking
end += flanking
if int(end) < int(
start): # if this target on minus strand flip the start/end
start, end = end, start
if chrom not in targets:
targets[chrom] = Intersecter()
if targets[chrom].find(start, end) == [] and abs(start - end) >= (
read_length * 2): # no overlaps yet
targets[chrom].add_interval(Interval(start, end))
unique_targets.append([chrom, start, end])
return unique_targets
def regionTree2(tmp,resFrag,strand,info,geneid):
if strand not in resFrag:
resFrag[strand] = {}
if tmp[0] in resFrag[strand]:
resFrag[strand][tmp[0]].add_interval(Interval(int(tmp[1]),int(tmp[2]),value={"exon":info,'geneid':geneid}))
else:
resFrag[strand][tmp[0]] = Intersecter()
resFrag[strand][tmp[0]].add_interval(Interval(int(tmp[1]),int(tmp[2]),value={"exon":info,'geneid':geneid}))
def regionTree(tmp, resFrag):
"""
tmp: The length of the list is at least 3(chrom,start,end)
resFrag: a dictionary to store the Interval tree
"""
if tmp[0] not in resFrag:
resFrag[tmp[0]] = Intersecter()
resFrag[tmp[0]].add_interval(Interval(int(tmp[1]), int(tmp[2]), tmp[3:]))
def __init__(self,coordinates):
self.interval_tree=dict()
for c in coordinates:
if c.chr_id not in self.interval_tree:
self.interval_tree[c.chr_id]=Intersecter()
self.interval_tree[c.chr_id].add_interval(Interval(c.bpstart,c.bpend,c))
def maps_gene(mapped):
'''Determine if the mapped alignment falls within a gene.'''
global intersecters
try:
intersecter = intersecters[mapped['genome']]
except KeyError:
genes = db.feature.find({'genome': mapped['genome'], 'type': 'gene'})
intersecter = Intersecter()
# Interval end is exclusive, need to +1 to line up with actual position
[intersecter.add_interval(Interval(gene['start'], gene['end'] + 1, gene['uid']))
for gene in genes]
intersecters[mapped['genome']] = intersecter
return intersecter.find(mapped['refStart'], mapped['refEnd'])
def load_BED(in_file, verbose=False):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
BED file are half-open, meaning that a bin ]100, 200] covered the bases 101 to 200
in_file = input file [character]
verbose = verbose mode [logical]
"""
x = {}
if verbose:
print "## Loading BED file '", in_file, "'..."
featureNames = []
nline = 0
with open(in_file) as bed_handle:
for line in bed_handle:
if nline > 0 and nline % 5000 == 0 and verbose:
print "## %d features loaded ..." % nline
nline += 1
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
print >> sys.stderr, "Warning : wrong input format in line", nline, ". Not a BED file !?"
continue
# BED files are zero-based, half-open as Intervals objects
start = int(start)
end = int(end)
featureNames.append(name.strip())
if chromosome in x:
tree = x[chromosome]
tree.add_interval(
Interval(start, end, value={'pos': nline - 1}))
else:
tree = Intersecter()
tree.add_interval(
Interval(start, end, value={'pos': nline - 1}))
x[chromosome] = tree
bed_handle.close()
return (x, featureNames)
def load_bed(in_file, verbose=False):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
intervals = {}
if verbose:
print >> sys.stderr, "## Loading BED file '", in_file, "'..."
bed_handle = open(in_file)
nline = 0
for line in bed_handle:
nline += 1
bedtab = line.strip().split("\t")
try:
chromosome, start, end = bedtab[:3]
except ValueError:
print >> sys.stderr, "Warning : wrong input format in line", nline, ". Not a BED file !?"
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
fragl = abs(end - start)
if chromosome in intervals:
tree = intervals[chromosome]
tree.add_interval(Interval(start, end))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end))
intervals[chromosome] = tree
bed_handle.close()
return intervals
def maps_gene(mapped):
"""Determine if the mapped alignment falls within a gene."""
global intersecters
try:
intersecter = intersecters[mapped['genome']]
except KeyError:
genes = db.feature.find({'genome': mapped['genome'], 'type': 'gene'})
intersecter = Intersecter()
# Interval end is exclusive, need to +1 to line up with actual position
[
intersecter.add_interval(
Interval(gene['start'], gene['end'] + 1, gene['uid']))
for gene in genes
]
intersecters[mapped['genome']] = intersecter
return intersecter.find(mapped['refStart'], mapped['refEnd'])
def load_BED(in_file, exclusionSize=0, verbose=False):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
x = {}
x_ex = {}
if verbose:
print "## Loading BED file '", in_file, "'..."
nline = 0
with open(in_file) as bed_handle:
for line in bed_handle:
nline +=1
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
print "Warning : wrong input format in line", nline,". Not a BED file !?"
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
name = name.strip()
if chromosome in x.keys():
tree = x[chromosome]
tree.add_interval(Interval(start, end, value={'name': name}))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end, value={'name': name}))
x[chromosome] = tree
## Exclusion regions
if exclusionSize > 0:
if chromosome in x_ex.keys():
tree_ex = x_ex[chromosome]
tree_ex.add_interval(Interval(start - int(exclusionSize), start, value={'name': str(name) + "_up"}))
tree_ex.add_interval(Interval(end, end + int(exclusionSize), value={'name': str(name) + "_dwn"}))
else:
tree_ex = Intersecter()
tree_ex.add_interval(Interval(start - int(exclusionSize), start, value={'name': str(name) + "_up"}))
tree_ex.add_interval(Interval(end, end + int(exclusionSize), value={'name': str(name) + "_dwn"}))
x_ex[chromosome] = tree_ex
bed_handle.close()
return (x, x_ex)
def get_reads_and_ranges(bam_region, cid, chrom, region_start, region_end, strand, options):
pos_range = defaultdict(lambda: [0,0])
filtered_reads = Intersecter()
read_iterator = filter_reads(
bam_region, options.chrom_prefix + chrom,
region_start, region_end, options
)
for read in read_iterator:
if is_valid_paired(read, region_start, options):
rstart = min(read.pos, read.pnext) + 1
rend = rstart + abs(read.isize) - 1
filtered_reads.add_interval(Interval(rstart, rend))
inc_pr(pos_range, rstart, rend, region_start, region_end)
inc_pr_at(pos_range, rstart, region_start, region_end)
inc_pr_at(pos_range, rend, region_start, region_end)
elif is_valid_single(read, options):
rstart = read.pos + 1
rend = rstart + aln_length(read.cigar) - 1
filtered_reads.add_interval(Interval(rstart, rend))
inc_pr(pos_range, rstart, rend, region_start, region_end)
if as_merged(read, options) or as_trimmed(read, options):
inc_pr_at(pos_range, rstart, region_start, region_end)
inc_pr_at(pos_range, rend, region_start, region_end)
elif read.is_reverse:
inc_pr_at(pos_range, rend, region_start, region_end)
else:
inc_pr_at(pos_range, rstart, region_start, region_end)
return filtered_reads, pos_range
def _index_record_in_intervaldict(self, rec):
'''
Insert CDS intervals from a chromosome SeqRecord into our cached
interval tree dict.
'''
intersector = self.intervaldict.setdefault(rec.id, Intersecter())
for feature in rec.features: # Each top-level CDS
intvl = dict(chrom=rec.id, value={'cdsobj': feature})
if hasattr(feature, 'strand'):
intvl['strand'] = feature.strand # could still be None.
locus = Interval(int(feature.location.start),
int(feature.location.end), **intvl)
intersector.add_interval(locus)
def purify_introns(Introns_Dict, Exons_Sect):
'''
select only introns that don't contain exons, these are likely to be "pure"
introns that lack any real polyA sites.
'''
pure = dict()
for (chrm, strand) in Introns_Dict.keys():
for intron in Introns_Dict[(chrm, strand)]:
if not Exons_Sect[(chrm, strand)].find(intron[0], intron[1]):
if not pure.has_key((chrm, strand)):
pure[(chrm, strand)] = Intersecter()
pure[(chrm, strand)].add(intron[0], intron[1], intron)
return pure
def calculate_score(chrom, start, end,ctype="WPS"):
filteredReads = Intersecter()
posRange = defaultdict(int)
for read in readIterator(args,chrom,start,end):
if read.is_duplicate or read.is_qcfail or read.is_unmapped: continue
if isSoftClipped(read.cigar): continue
if read.is_paired:
if read.mate_is_unmapped: continue
if read.rnext != read.tid: continue
if read.is_read1 or (read.is_read2 and read.pnext+read.qlen < start):
if read.isize == 0: continue
if options.downsample != None and random.random() >= options.downsample: continue
rstart = min(read.pos,read.pnext)+1 # 1-based
rend = rstart+abs(read.isize)-1 # end included
rlength = rend-rstart+1
if options.minLength <= rlength <= options.maxLength:
filteredReads.add_interval(Interval(rstart,rend))
if ctype == "COV":
for i in range(rstart,rend+1):
if i >= start and i <= end:
posRange[i]+=1
elif ctype == "STARTS":
if rstart >= start and rstart <= end:
posRange[rstart]+=1
if rend >= start and rend <= end:
posRange[rend]+=1
else:
if options.downsample != None and random.random() >= options.downsample: continue
rstart = read.pos+1 # 1-based
rend = rstart+aln_length(read.cigar)-1 # end included
rlength = rend-rstart+1
if options.minLength <= rlength <= options.maxLength:
filteredReads.add_interval(Interval(rstart,rend))
if ctype == "COV":
for i in range(rstart,rend+1):
if i >= start and i <= end:
posRange[i]+=1
elif ctype == "STARTS":
if rstart >= start and rstart <= end:
posRange[rstart]+=1
if rend >= start and rend <= end:
posRange[rend]+=1
if ctype == "WPS":
protection = options.protection//2
for pos in xrange(start,end+1):
rstart,rend = pos-protection,pos+protection
gcount,bcount = 0,0
for read in filteredReads.find(rstart,rend):
if (read.start > rstart) or (read.end < rend): bcount +=1
else: gcount +=1
posRange[pos]+=gcount-bcount
res = []
for pos in xrange(start,end+1):
res.append(posRange[pos])
return res
def GenomicInterval_2_intersecter_and_dict(GI):
II = dict()
ID = dict()
for intron in GI:
chrm = clean_chr_name(intron.chr)
strand = intron.strand
if not II.has_key((chrm, strand)):
II[(chrm, strand)] = Intersecter()
II[(chrm, strand)].add(intron.start, intron.stop,
[intron.start, intron.stop])
if not ID.has_key((chrm, intron.strand)):
ID[(chrm, strand)] = []
ID[(chrm, strand)].append([intron.start, intron.stop])
return II, ID
def polyA_dict_2_intersecter( polyA ):
'''
load a polyA gff file into a dictionary/intersecter object
NOTE: bx.python is (open,open) in its interval searchers,
e.g. T.find( 1,10 ) will not return true if T contains (1,1) or (10,10)
'''
polyA_I = dict()
for (chrm, strand) in polyA.keys():
if not polyA_I.has_key((chrm,strand)):
polyA_I[(chrm,strand)] = Intersecter()
for p_site in polyA[(chrm,strand)]:
polyA_I[(chrm,strand)].add(
p_site, p_site, [p_site, polyA[(chrm,strand)][p_site]] )
return polyA_I
def load_restriction_fragment(in_file, verbose):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
resFrag = {}
if verbose:
print "## Loading Restriction File Intervals '", in_file, "'..."
bed_handle = open(in_file)
for line in bed_handle:
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
# FIXME we might want a proper warning message here !
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
name = name.strip()
if chromosome in resFrag.keys():
tree = resFrag[chromosome]
tree.add_interval(Interval(start, end, value={'name': name}))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end, value={'name': name}))
resFrag[chromosome] = tree
bed_handle.close()
return resFrag
def index_bed(genes, un_stranded):
""" """
chroms = set([i['chrom'] for i in genes])
if not un_stranded:
bed_quicksect = {
chr + ":" + str: Intersecter()
for str in ['+', '-'] for chr in set(chroms)
}
else:
bed_quicksect = {chr: Intersecter() for chr in set(chroms)}
for annotation in genes:
chrom = annotation['chrom']
strand = annotation['strand']
contig = chrom if un_stranded else chrom + ":" + strand
bed_quicksect[contig].insert_interval(
Interval(annotation['beg'],
annotation['end'],
chrom=chrom,
strand=strand,
value={
"annotation_type": annotation['annotation_type'],
"annotation_name": annotation['annotation_name'],
}))
return bed_quicksect
def gtf_CDSs_2_intersecter_and_dict(gtf_fn):
fid = open(gtf_fname)
CDS_I = dict()
CDS_D = dict()
for line in fid:
data = line.strip().split('\t')
if not data[2] == 'CDS':
continue
chrm = clean_chr_name(data[0])
strand = data[6]
start = int(data[3])
end = int(data[4])
if not CDS_I.has_key((chrm, strand)):
CDS_I[(chrm, strand)] = Intersecter()
CDS_I[(chrm, strand)].add(start, end, [start, end])
if not CDS_D.has_key((chrm, strand)):
CDS_D[(chrm, strand)] = []
CDS_D[(chrm, strand)].append([start, end])
return CDS_I, CDS_D
def emf_init_index(filename):
from bx.intervals.intersection import Intersecter, Interval
if os.path.isfile(filename):
infile = open(filename)
res = {}
for line in infile:
if line.startswith("#"): continue
fields = line.split() #Chr\tStart\tEnd\tFile\tByte\tLine
if len(fields) == 6:
chrom,start,end,cfile,bytes,lines = fields
start,end = int(start)+1,int(end)+1 #MAKE COORDINATES ONE BASED HALF-OPEN
if chrom not in res:
res[chrom] = {}
res[chrom]["coords"] = Intersecter()
res[chrom]["coords"].add_interval(Interval(start, end))
res[chrom][(start,end)] = cfile,int(bytes),int(lines)
else:
sys.stderr.write("Unexpected line [%s]: %s"%(filename,line))
infile.close()
return res
return None
def calculate_intersection(cls,coords1,coords2,build_matrix=False):
coords_in_common=set()
intersection_indexes=set()
if build_matrix:
intersection_matrix=sparse_matrix((len(coords1),len(coords2)))
coord_to_row_index=dict()
row_index=0
interval_tree=dict()
#Build the interval tree on the first set of coordinates
for c in coords1:
if c.chr_id not in interval_tree:
interval_tree[c.chr_id]=Intersecter()
interval_tree[c.chr_id].add_interval(Interval(c.bpstart,c.bpend))
coord_to_row_index[c]=row_index
row_index+=1
#Calculating the intersection
#for each coordinates on the second set check intersection and fill the matrix
for cl_index,c in enumerate(coords2):
if interval_tree.has_key(c.chr_id):
coords_hits=interval_tree[c.chr_id].find(c.bpstart, c.bpend)
#coords_in_common+=coords_hits
for coord_hit in coords_hits:
c_to_add=Coordinate.coordinates_from_interval(c.chr_id, coord_hit)
coords_in_common.add(c_to_add)
row_index=coord_to_row_index[c_to_add]
intersection_indexes.add(row_index)
if build_matrix:
intersection_matrix[row_index,cl_index]+=1
if build_matrix:
return list(coords_in_common),list(intersection_indexes),intersection_matrix
else:
return list(coords_in_common),list(intersection_indexes)
def annotate(self):
#allocate_memory
self.annotation_track=np.ones(len(self.input_coordinates),dtype=np.int)
self.interval_tree=dict()
self.coord_to_row_index=dict()
self.row_index=0
#Build the interval Tree
for c in self.input_coordinates:
if c.chr_id not in self.interval_tree:
self.interval_tree[c.chr_id]=Intersecter()
self.interval_tree[c.chr_id].add_interval(Interval(c.bpstart,c.bpend))
self.coord_to_row_index[c]=self.row_index
self.row_index+=1
for idx,bed_filename in enumerate(self.annotations_filenames):
coordinates=Coordinate.bed_to_coordinates(bed_filename)
prime_number=self.annotation_names_to_prime[self.annotation_names[idx]]
for idx_intersection in self.__intersection_indexes(coordinates):
self.annotation_track[idx_intersection]*=prime_number
def load_restriction_fragment(enzyme_bed):
"""
Read enzyme bed file and store the intervals in a tree
:param enzyme_bed: bed file path
:return: res_frag
"""
res_frag = defaultdict(lambda :Intersecter())
with open(enzyme_bed) as fp:
for nline, line in enumerate(fp, 1):
line_list = line.strip().split()
try:
chrn, start, end, name = line_list[:4]
except ValueError:
print("[Warning] wrong input format in line :{}. "
"Not a bed file?!".format(nline))
continue
start = int(start)
end = int(end)
tree = res_frag[chrn]
tree.add_interval(Interval(start, end, value={'name':name}))
return res_frag
# fields three and six are set to default value '-'
# field 8 is set to default value '.' to meet compatibility with GFF3
f1.columns = [
'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase',
'attributes'
]
f2 = pd.read_csv(sys.argv[2], header=None, sep="\t")
f2.columns = [
'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase',
'attributes'
]
tree_dict = {}
tree = Intersecter()
# first input file - gvf file containing the annotation
for chrom in range(1, 23):
tree_dict['chr' + str(chrom)] = Intersecter()
tree_dict['chrX'] = Intersecter()
tree_dict['chrY'] = Intersecter()
gene_id_re = re.compile("(GeneID=[0-9]+)")
gene_symbol = re.compile("(GeneSymbol=[A-z0-9]+)")
for i, j in f1.iterrows():
geneid = gene_id_re.search(j[-1]).group(0)
geneid_new = geneid.replace("GeneID=", "")
genesymbol = gene_symbol.search(j[-1]).group(0)
def load_BED(in_file, exclusionSize=0, verbose=False):
"""
Read a BED file and store the intervals in a tree
Intervals are zero-based objects. The output object is a hash table with
one search tree per chromosome
in_file = input file [character]
verbose = verbose mode [logical]
"""
x = {}
x_ex = {}
if verbose:
print "## Loading BED file '", in_file, "'..."
nline = 0
with open(in_file) as bed_handle:
for line in bed_handle:
nline += 1
bedtab = line.split("\t")
try:
chromosome, start, end, name = bedtab[:4]
except ValueError:
print "Warning : wrong input format in line", nline, ". Not a BED file !?"
continue
# BED files are zero-based as Intervals objects
start = int(start) # + 1
end = int(end)
name = name.strip()
if chromosome in x:
tree = x[chromosome]
tree.add_interval(Interval(start, end, value={'name': name}))
else:
tree = Intersecter()
tree.add_interval(Interval(start, end, value={'name': name}))
x[chromosome] = tree
## Exclusion regions
if exclusionSize > 0:
if chromosome in x_ex:
tree_ex = x_ex[chromosome]
tree_ex.add_interval(
Interval(start - int(exclusionSize),
start,
value={'name': str(name) + "_up"}))
tree_ex.add_interval(
Interval(end,
end + int(exclusionSize),
value={'name': str(name) + "_dwn"}))
else:
tree_ex = Intersecter()
tree_ex.add_interval(
Interval(start - int(exclusionSize),
start,
value={'name': str(name) + "_up"}))
tree_ex.add_interval(
Interval(end,
end + int(exclusionSize),
value={'name': str(name) + "_dwn"}))
x_ex[chromosome] = tree_ex
bed_handle.close()
return (x, x_ex)
mdict = {}
for i in gffs:
k = gffs.index(i)
syn_region[k] = {}
for y in i:
if k == 0:
if y.name.startswith('GRMZM'):
y.name = y.name.split('.')[0]
else:
y.name = '_'.join(y.name.split('.')[:2])
if k == 1 or k == 2:
y.name = '.'.join(y.name.split('.')[:2])
if y[2] != 'gene': continue
if y.name not in syn[k]: continue
if y[0] not in syn_region[k]:
syn_region[k][y[0]] = Intersecter()
syn_region[k][y[0]].add_interval(Interval(int(y[3]), int(y[4]),
y.name))
if y.name not in mdict:
mdict[y.name] = []
# if '_' in y.name:continue
# if 'scaffold' in y.chrom:continue
mdict[y.name].append(y.chrom)
mdict[y.name].append(int(y[3]))
mdict[y.name].append(int(y[4]))
mdict[y.name].append(y.strand)
cand = open(sys.argv[2])
count = 0
for line in cand:
count += 1
chrom = options.region.split(':')[0]
start,end = map(int,options.region.split(':')[1].replace(",","").split("-"))
outchrom = chrom
outchrom = outchrom.replace("chr","")
if outchrom.startswith('gi|'): # gi|224589803|ref|NC_000012.11|
NCfield = outchrom.split("|")[-2]
if NCfield.startswith("NC"):
outchrom = "%d"%(int(NCfield.split(".")[0].split("_")[-1]))
if options.verbose:
sys.stderr.write("Coordinates parsed: Chrom %s Start %d End %d\n"%(chrom,start,end))
except:
sys.stderr.write("Error: Region not defined in a correct format!")
sys.exit()
posRange = defaultdict(lambda:[0,0,0])
filteredReads = Intersecter()
for read in readIterator(args,options):
if read.is_duplicate or read.is_qcfail or read.is_unmapped: continue
if isSoftClipped(read.cigar): continue
if read.is_paired:
if read.mate_is_unmapped: continue
if read.rnext != read.tid: continue
if read.is_read1 or (not options.pipe and read.is_read2 and read.pnext+read.qlen < start):
if read.isize == 0: continue
if options.downsample != None and random.random() >= options.downsample: continue
if options.random:
rstart = min(read.pos,read.pnext)+1+random.randint(-5,5) # 1-based
rend = rstart+abs(read.isize)-1+random.randint(-5,5) # end included
else:
rstart = min(read.pos,read.pnext)+1 # 1-based
trees = dict()
with gzip.open(args.subject) if args.subject.endswith('.gz') else open(
args.subject) as fh:
genome = ''
for line in fh:
if line.isspace() or line[0] == '#':
continue
data = line.rstrip().split('\t')
if len(data) != 9:
sys.stderr.write('number of columns != 9: {}'.format(line))
g, start, end, strand = data[0], int(data[3]), int(data[4]), data[6]
if g != genome:
genome = g
trees[genome] = Intersecter()
if strand == '+':
start -= args.extend_upstream
end += args.extend_downstream
else:
start -= args.extend_downstream
end += args.extend_upstream
if not args.embeded and strand == '-': # complement strand
start, end = -end, -start
trees[genome].add_interval(Interval(start, end, value=data))
if args.split:
if args.split_dir is None:
outdir = '{}.intersect@{}'.format(
def read_chain_file(chain_file, print_table=False):
'''
Read chain file.
Parameters
----------
chain_file : file
Chain format file. Input chain_file could be either plain text, compressed file
(".gz",".Z", ".z", ".bz", ".bz2", ".bzip2"), or a URL pointing to the chain file
("http://","https://", "ftp://"). If url was used, chain file must be plain text.
print_table : bool, optional
Print mappings in human readable table.
Returns
-------
maps : dict
Dictionary with source chrom name as key, IntervalTree object as value. An
IntervalTree contains many intervals. An interval is a start and end position
and a value. eg. Interval(11, 12, strand="-", value = "abc")
target_chromSize : dict
Chromosome sizes of target genome
source_chromSize : dict
Chromosome sizes of source genome
'''
logging.info("Read the chain file \"%s\" " % chain_file)
maps = {}
target_chromSize = {}
source_chromSize = {}
if print_table:
blocks = []
for line in ireader.reader(chain_file):
# Example: chain 4900 chrY 58368225 + 25985403 25985638 chr5 151006098 - 43257292 43257528 1
if not line.strip():
continue
line = line.strip()
if line.startswith(('#', ' ')): continue
fields = line.split()
if fields[0] == 'chain' and len(fields) in [12, 13]:
#score = int(fields[1]) # Alignment score
source_name = fields[2] # E.g. chrY
source_size = int(fields[3]) # Full length of the chromosome
source_strand = fields[4] # Must be +
if source_strand != '+':
raise Exception(
"Source strand in a chain file must be +. (%s)" % line)
source_start = int(fields[5]) # Start of source region
#source_end = int(fields[6]) # End of source region
target_name = fields[7] # E.g. chr5
target_size = int(fields[8]) # Full length of the chromosome
target_strand = fields[9] # + or -
target_start = int(fields[10])
#target_end = int(fields[11])
target_chromSize[target_name] = target_size
source_chromSize[source_name] = source_size
if target_strand not in ['+', '-']:
raise Exception("Target strand must be - or +. (%s)" % line)
#chain_id = None if len(fields) == 12 else fields[12]
if source_name not in maps:
maps[source_name] = Intersecter()
sfrom, tfrom = source_start, target_start
# Now read the alignment chain from the file and store it as a list (source_from, source_to) -> (target_from, target_to)
elif fields[0] != 'chain' and len(fields) == 3:
size, sgap, tgap = int(fields[0]), int(fields[1]), int(fields[2])
if print_table:
if target_strand == '+':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, tfrom, tfrom + size, target_strand))
elif target_strand == '-':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand))
if target_strand == '+':
maps[source_name].add_interval(
Interval(
sfrom, sfrom + size,
(target_name, tfrom, tfrom + size, target_strand)))
elif target_strand == '-':
maps[source_name].add_interval(
Interval(sfrom, sfrom + size,
(target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand)))
sfrom += size + sgap
tfrom += size + tgap
elif fields[0] != 'chain' and len(fields) == 1:
size = int(fields[0])
if print_table:
if target_strand == '+':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, tfrom, tfrom + size, target_strand))
elif target_strand == '-':
blocks.append(
(source_name, sfrom, sfrom + size, source_strand,
target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand))
if target_strand == '+':
maps[source_name].add_interval(
Interval(
sfrom, sfrom + size,
(target_name, tfrom, tfrom + size, target_strand)))
elif target_strand == '-':
maps[source_name].add_interval(
Interval(sfrom, sfrom + size,
(target_name, target_size - (tfrom + size),
target_size - tfrom, target_strand)))
else:
raise Exception("Invalid chain format. (%s)" % line)
#if (sfrom + size) != source_end or (tfrom + size) != target_end:
# raise Exception("Alignment blocks do not match specified block sizes. (%s)" % header)
if print_table:
for i in blocks:
print('\t'.join([str(n) for n in i]))
return (maps, target_chromSize, source_chromSize)
def compare_two_transcripts(trans1, trans2, transcript_dict,
afe=False):
"""
Returns the splice differences between two transcripts.
Single exon-comparisons are ignored.
Parameters
----------
trans1 : string
transcript of interest
trans2 : string
second transcript of interest
transcript_dict : a dictionary of transcript names with
values being a list of exons
afe : bool
whether to include alternate start and ends
:TODO make a better return
:TODO maybe include something similar to to_plot
Returns
-------
Exclusive Junctions :
5' upstream exons :
3' downstram exons :
Skipped Exons : Diffevent
"""
# TODO refactor this
t1 = transcript_dict[trans1]
t2 = transcript_dict[trans2]
tree = Intersecter()
starts1 = [i[0] for i in t1]
starts2 = [i[0] for i in t2]
reverse = False
if min(starts1) <= min(starts2):
s1 = t1
s2 = t2
s2_beg = min(starts2)
else:
s1 = t2
s2 = t1
reverse = True
s2_beg = min(starts1)
if reverse: torder = (trans2, trans1)
else: torder = (trans1, trans2)
# Ignore single-exon stuff
if len(s1) <= 1 or len(s2) <= 1:
return([], [])
for i in s1:
tree.add_interval(Interval(int(i[0]), int(i[1]),
value={'anno':i[2]}))
matching_exons = []
exclusive_juncs = []
skipped_exons = []
altends = []
exon_match = {}
s1.sort(key=lambda x: x[0])
s2.sort(key=lambda x: x[0])
max_exon_1 = s1[-1][2]
max_exon_2 = s2[-1][2]
#end_position_s2 = max([i[1] for i in s2])
s1_end = max([i[1] for i in s1])
prev_match = None
if max_exon_1 < s1[0][2]:
strand = -1
else:
strand = 1
for pcurr in range(len(s2)):
start, end, exon_n = s2[pcurr]
overlap = tree.find(int(start), int(end))
if len(overlap) == 0:
if prev_match and (start < s1_end):
#skipped exons
cigar = _generate_cigar(s2, pcurr, mskip=1)
try:
if exon_match[exon_n - strand] == prev_match.value['anno']:
try:
nm = tree.find(*s2[pcurr + 1][0:2])[0]
ocigar = [(3, nm.start - prev_match.end)]
nexon = nm.value['anno']
except IndexError:
nm=s1[_get_by_exonn(prev_match.value['anno']+strand,s1)]
ocigar = [(3,nm[0] - prev_match.end)]
nexon = nm[2]
skipped_exons.append(DiffEvent('skipped_exon', start, end,
torder, cigar2=cigar, cigar1 = ocigar,
exon_num = (None, exon_n),
exon2=(prev_match.value['anno'], nexon))
)
except KeyError:
# Multiple skipped exons
ncig = _generate_cigar(s2, pcurr, mskip=1)[1:]
skipped_exons[-1]._extend(ncig, cig=2)
elif start > s1_end:
if prev_match:
cigar = _generate_cigar(s2, pcurr, mskip=1)
pm = tree.find(*s2[pcurr - 1][0:2])[0]
pexon = pm.value['anno']
ocigar = []
for i in range(pexon, max_exon_1+strand, strand):
narg = _get_by_exonn(i, s1)
ocigar.append((0, s1[narg][0], s1[narg][1]))
try:
ocigar.append((3, s1[narg][1] - s1[narg+1][0]))
except IndexError:
pass
#:TODO extend ocigar till end?
altends.append(DiffEvent('AE', start, end,
torder, cigar2=cigar, cigar1=ocigar,
exon_num = (None, exon_n)))
else:
pass
else:
# Alternate start site that starts in between exons
# of other transcript
cigar = _generate_cigar(s2, pcurr, mskip=1)[:-1]
try:
nm = tree.find(*s2[pcurr + 1][0:2])[0]
except IndexError:
from IPython import embed
embed()
nexon = nm.value['anno']
narg = _get_by_exonn(nexon - strand, s1)
pmatch = s1[narg]
ocigar = [(0, pmatch[1] - pmatch[0]),
(3, nm.start - pmatch[1])]
altends.append(DiffEvent('AS', start, end,
torder, cigar2=cigar, cigar1 = ocigar))
elif len(overlap) == 1:
if start == overlap[0].start and end == overlap[0].end:
s1_exon_n = overlap[0].value['anno']
matching_exons.append((start, end, (s1_exon_n,
exon_n), (0, 0)))
if prev_match:
if s1_exon_n - prev_match.value['anno'] == strand:
pass
else:
# Difference in exon matches
mskip = abs(s1_exon_n - prev_match.value['anno'] ) - 1
narg = _get_by_exonn(prev_match.value['anno']+strand, s1)
s_s1 = s1[narg] # skipped s1
cigar = _generate_cigar(s1, narg, mskip=mskip)
ocigar = [(3, start - s2[pcurr-1][1])]
# Remove previous one
skipped_exons.append(
DiffEvent('skipped_exon',
s_s1[0], s_s1[1], torder,
cigar2 = ocigar, cigar1 = cigar,
exon_num = (s_s1[2], None),
exon2 = (exon_n-strand, exon_n)))
prev_match = overlap[0]
else:
sstart = min(start, overlap[0].start)
ssend = max(end, overlap[0].end)
# Ignore 5' or 3' differences
if (exon_n == max_exon_2 and
overlap[0].value['anno'] == max_exon_1):
if end == overlap[0].end:
prev_match = overlap[0]
else:
exclusive_juncs.append(
(sstart, ssend,
(overlap[0].value['anno'], exon_n),
(overlap[0].start - start, overlap[0].end - end) ))
# Deal with partial matches
prev_match = overlap[0]
exon_match[exon_n] = int(overlap[0].value['anno'])
else:
pass
skipped_exons = EventCollection(transcript_ids = [s1, s2], events=skipped_exons)
skipped_exons.events.extend(altends)
return(matching_exons, skipped_exons)
if options.pipe: ## if -p specified, pass file along pipe without writing
outfile = sys.stdout
elif options.outdir != None: ## otherwise, write to output file
outfilepath = os.path.join(os.getcwd(), options.outdir + "/" + outfilename)
directory = os.path.dirname(outfilepath) ## get the directory full path
if not os.path.exists(directory): ## check if it exists
os.makedirs(directory) ## if not, create the directory
outfile = open(outfilepath, "w+") ## write the file to the directory
else:
outfile = open(outfilename, "w+") ## otherwise, write to current dir
"""
Handle data
"""
total_reads = 0
start_end_list = Intersecter(
) ## list to hold start/end of each read in infile
init_pos = 0 ## for defining region if user does not
final_pos = 0 ## for defining region if user does not
read_start = 0 ## start of each read
read_end = 0 ## end of each read
other_read_end = 0
"""
Main functionality:
"""
for read in infile:
total_reads += 1
## get start position of the first read
def generate(x):
"Generates random interval over a size and span"
lo = randint(10000, SIZE)
hi = lo + randint(1, randint(1, 10**4))
return (lo, hi)
def generate_point(x):
lo = randint(10000, SIZE)
return (lo, lo)
# use this to force both examples to generate the same data
seed(10)
# generate 10 thousand random intervals
data = map(generate, xrange(N))
# generate the intervals to query over
query = map(generate_point, xrange(1000))
# create the interval tree
tree = Intersecter()
# build an interval tree from the rest of the data
for start, end in data:
tree.add_interval( Interval(start, end) )
# perform the query
for q, q in query:
overlap = tree.find(q, q)
out = [ (x.start, x.end) for x in overlap ]
print '(%s) -> %s' % (q, out)