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()
stop_err(
'Invalid genome build, this tool currently only works with data from build hg17. Click the pencil icon in your history item to correct the build if appropriate.'
)
# Open the h5 file
h5 = openFile(h5_fname, mode="r")
# Load intervals and names for the subregions
intersecters = {}
for i, line in enumerate(file(mapping_fname)):
line = line.rstrip('\r\n')
if line and not line.startswith('#'):
chr, start, end, name = line.split()[0:4]
if not intersecters.has_key(chr):
intersecters[chr] = intervals.Intersecter()
intersecters[chr].add_interval(
intervals.Interval(int(start), int(end), name))
# Find the subregion containing each input interval
skipped_lines = 0
first_invalid_line = 0
invalid_line = ''
out_file = open(out_fname, "w")
warnings = []
warning = ''
for i, line in enumerate(file(in_fname)):
line = line.rstrip('\r\n')
if line.startswith('#'):
if i == 0:
out_file.write("%s\tscore\n" % line)
else:
out_file.write("%s\n" % line)
