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"""
Iterator for the BED format ( http://genome.ucsc.edu/FAQ/FAQformat.html#format1 )
Returns chrom, chromStart, chromEnd, name, score
"""
cdef class BedReader:
cdef object f
def __init__( self, f ):
self.f = f
def __iter__( self ):
return self
def __next__( self ):
while True:
line = self.f.readline()
if not line:
raise StopIteration()
if line.isspace():
continue
if line[0] == "#":
continue
if line[0].isalpha():
if line.startswith( "track" ) or line.startswith( "browser" ):
continue
feature = line.strip().split()
chrom = feature[0]
chrom_start = int(feature[1])
chrom_end = int(feature[2])
if len(feature) > 3:
name = feature[3]
else:
name = None
if len(feature) > 4:
score = int(feature[4])
else:
score = None
return chrom, chrom_start, chrom_end, name, score
else:
raise "Unexpected input line: %s" % line.strip()
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