def read_dir(self, d):
lookup = dict()
scores_by_what = dict()
if not os.path.exists(d):
for p in DATA_SEARCH_PATH:
if os.path.exists(os.path.join(p, d)):
d = os.path.join(p, d)
break
for file in os.listdir(d):
if file.endswith(".match"):
for line in (open(os.path.join(d, file))):
if line.startswith("#"): continue
line = line.strip()
f = line.split()
if len(f) >= 4:
chr, start, end, what = f[0:4]
else:
continue
if not chr in lookup: lookup[chr] = intervals.Intersecter()
lookup[chr].add_interval(
intervals.Interval(int(start), int(end), what))
else:
k = file.split('.')[0]
if not k in scores_by_what:
scores_by_what[k] = FileBinnedArray(
open(os.path.join(d, file)))
if lookup == {}:
self.lookup = None
self.scores = scores_by_what
#return None, scores_by_what
else:
self.lookup = lookup
self.scores = scores_by_what
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
try:
range_filename = args[0]
refindex = int(args[1])
if options.mincols: mincols = int(options.mincols)
else: mincols = 10
except:
doc_optparse.exit()
# Load Intervals
intersecter = intervals.Intersecter()
for line in file(range_filename):
fields = line.split()
intersecter.add_interval(
intervals.Interval(int(fields[0]), int(fields[1])))
# Start axt on stdout
out = bx.align.axt.Writer(sys.stdout)
# Iterate over input axt
for axt in bx.align.axt.Reader(sys.stdin):
ref_component = axt.components[refindex]
# Find overlap with reference component
intersections = intersecter.find(ref_component.start,
ref_component.end)
# Keep output axt ordered
intersections.sort()
# Write each intersecting block
for interval in intersections:
start = max(interval.start, ref_component.start)
end = min(interval.end, ref_component.end)
sliced = axt.slice_by_component(refindex, start, end)
good = True
for c in sliced.components:
if c.size < 1:
good = False
if good and sliced.text_size > mincols: out.write(sliced)
# Close output axt
out.close()
def main():
intersecters = {}
# Read ranges
for chr, start, end in read_intervals( misc.open_compressed( sys.argv[1] ) ):
if not intersecters.has_key( chr ): intersecters[ chr ] = intervals.Intersecter()
intersecters[ chr ].add_interval( intervals.Interval( start, end ) )
# Count intersection
total = 0
for chr, start, end in read_intervals( misc.open_compressed( sys.argv[2] ) ):
if intersecters.has_key( chr ):
intersection = intersecters[ chr ].find( start, end )
if intersection:
#print chr, intersection
total += 1
print total
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
try:
assert len(args) > 0
except:
doc_optparse.exit()
# Load Intervals
intersector = intervals.Intersecter()
for f in args:
for line in file(f):
if line.startswith("#") or line.isspace(): continue
fields = line.split()
intersector.add_interval(
intervals.Interval(int(fields[0]), int(fields[1])))
# Start MAF on stdout
out = bx.align.maf.Writer(sys.stdout)
# Iterate over input MAF
for maf in bx.align.maf.Reader(sys.stdin):
# Find overlap with reference component
intersections = intersector.find(maf.components[0].start,
maf.components[0].end)
# Write only if no overlap
if len(intersections) == 0:
out.write(maf)
# Close output MAF
out.close()
def __main__():
# Parse Command Line
options, args = doc_optparse.parse( __doc__ )
try:
range_filename = args[ 0 ]
try:
refindex = int( args[ 1 ] )
refname = None
except:
refindex = None
refname = args[ 1 ]
if options.mincols: mincols = int( options.mincols )
else: mincols = 10
if options.prefix: prefix = options.prefix
else: prefix = ""
except:
doc_optparse.exit()
# Load Intervals
intersecters = dict()
for line in file( range_filename ):
fields = line.split()
src = prefix + fields[0]
if not src in intersecters: intersecters[src] = intervals.Intersecter()
intersecters[src].add_interval( intervals.Interval( int( fields[1] ), int( fields[2] ) ) )
# Start MAF on stdout
out = bx.align.maf.Writer( sys.stdout )
# Iterate over input MAF
for maf in bx.align.maf.Reader( sys.stdin ):
if refname:
sourcenames = [ cmp.src.split('.')[0] for cmp in maf.components ]
try: refindex = sourcenames.index( refname )
except:
continue
ref_component = maf.components[ refindex ]
# Find overlap with reference component
if not ( ref_component.src in intersecters ): continue
intersections = intersecters[ ref_component.src ].find( ref_component.start, ref_component.end )
# Keep output maf ordered
intersections.sort()
# Write each intersecting block
for interval in intersections:
start = max( interval.start, ref_component.start )
end = min( interval.end, ref_component.end )
sliced = maf.slice_by_component( refindex, start, end )
good = True
for c in sliced.components:
if c.size < 1:
good = False
if good and sliced.text_size > mincols: out.write( sliced )
# Close output MAF
out.close()
def main():
if len(sys.argv) < 5:
print >> sys.stderr, "%s bedfile inmaf spec1,spec2,... motif_file " % sys.argv[
0]
sys.exit(0)
# read in intervals
regions = {}
for line in open(sys.argv[1]):
if line.startswith('#'): continue
fields = line.strip().split()
chrom, start, end = fields[0], int(fields[1]), int(fields[2])
try:
name = fields[3]
except:
name = None
if chrom not in regions: regions[chrom] = intervals.Intersecter()
regions[chrom].add(start, end, name)
pwm = {}
for wm in pwmx.Reader(open(sys.argv[4])):
pwm[wm.id] = wm
print >> sys.stderr, wm.id, len(wm)
inmaf = open(sys.argv[2])
threshold = 0.5
species = []
for sp in sys.argv[3].split(','):
species.append(sp)
for maf in align_maf.Reader(inmaf):
mafchrom = maf.components[0].src.split('.')[1]
mafstart = maf.components[0].start
mafend = maf.components[0].end
reftext = maf.components[0].text
# maf block scores for each matrix
for scoremax, width, headers in MafBlockScorer(pwm, species, maf):
#print >>sys.stderr,headers
blocklength = width
mafsrc, mafstart, mafend = headers[0]
mafchrom = mafsrc.split('.')[1]
# lists of scores for each position in scoremax
for mx_name, mx in scoremax.items():
#print >>sys.stderr, mx_name, len(pwm[mx_name])
for offset in range(blocklength):
# scan all species with threshold
for i in range(len(species)):
if mx[i][offset] > threshold:
refstart = mafstart + offset - reftext.count(
'-', 0, offset)
refend = refstart + len(pwm[mx_name])
data = " ".join([
"%.2f" % mx[x][offset]
for x in range(len(species))
])
# quote the motif
r = regions[mafchrom].find(refstart, refend)
if mafchrom in regions and len(r) > 0:
region_label = r[0].value
else:
#region_label = 0
continue
v_name = mx_name.replace(' ', '_')
print mafchrom, refstart, refend, region_label, v_name, data
break
sys.exit()
##### INPUTS AND OUTPUTS #####
# get intervals
print "Loading data..."
p1_ints = np.loadtxt(options.i, 'str', delimiter="\t")
print "Calculating rank..."
# save as fast lookup
bedInts = {}
for j in range(0, len(p1_ints)):
chr = p1_ints[j][0]
start = int(p1_ints[j][1])
end = int(p1_ints[j][2])
if not bedInts.has_key(chr):
bedInts[chr] = intervals.Intersecter()
bedInts[chr].insert(start, end, np.append(p1_ints[j], j))
# pass filter idx
idx = np.array(np.ones(len(p1_ints)), dtype=int)
##### SCRIPT #####
# loop through files
print "Looping through intervals..."
for i in range(0, len(p1_ints)):
# look for overlaps
atacChr = p1_ints[i][0]
atacStart = int(p1_ints[i][1])
atacEnd = int(p1_ints[i][2])
# if pass filter and only 1 match
def main():
if len(sys.argv) < 5:
print("%s bedfile inmaf spec1,spec2,... string [string2,...]" %
sys.argv[0],
file=sys.stderr)
sys.exit(0)
# read in intervals
regions = {}
for line in open(sys.argv[1]):
if line.startswith('#'):
continue
fields = line.strip().split()
chrom, start, end = fields[0], int(fields[1]), int(fields[2])
try:
name = fields[3]
except IndexError:
name = None
if chrom not in regions:
regions[chrom] = intervals.Intersecter()
regions[chrom].add(start, end, name)
motif_strings = sys.argv[4:]
if not isinstance(motif_strings, list):
motif_strings = [motif_strings]
inmaf = open(sys.argv[2])
threshold = 0.5
species = []
for sp in sys.argv[3].split(','):
species.append(sp)
for maf in align_maf.Reader(inmaf):
mafchrom = maf.components[0].src.split('.')[1]
mafstart = maf.components[0].start
mafend = maf.components[0].end
reftext = maf.components[0].text
r = regions[mafchrom].find(mafstart, mafend)
if mafchrom not in regions or len(r) == 0:
continue
# maf block scores for each matrix
for scoremax, width, headers in MafMotifScorer(species, maf,
motif_strings):
blocklength = width
mafsrc, mafstart, mafend = headers[0]
mafchrom = mafsrc.split('.')[1]
# lists of scores for each position in scoremax
for mx_name, mx in scoremax.items():
for offset in range(blocklength):
# scan all species with threshold
for i in range(len(species)):
if mx[i][offset] > threshold:
refstart = mafstart + offset - reftext.count(
'-', 0, offset)
refend = refstart + len(mx_name)
data = " ".join([
"%.2f" % mx[x][offset]
for x in range(len(species))
])
# quote the motif
r = regions[mafchrom].find(refstart, refend)
if mafchrom in regions and len(r) > 0:
region_label = r[0].value
else:
# region_label = 0
continue
v_name = mx_name.replace(' ', '_')
print(mafchrom, refstart, refend, region_label,
v_name, data)
break
