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"""
Support for scores in the `wiggle`_ file format used by the UCSC Genome
Browser.
The positions in the wiggle format are 1-relative, however,
the positions returned match the BED/interval format which is zero-based, half-open.
.. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
"""
def parse_header( line ):
return dict( [ field.split( '=' ) for field in line.split()[1:] ] )
cdef class WiggleReader:
"""
Iterator yielding chrom, start, end, strand, value.
Values are zero-based, half-open.
Regions which lack a score are ignored.
"""
#cdef object file
#cdef object current_chrom
#cdef long current_pos
#cdef long current_step
#cdef long current_span
#cdef linemode mode
def __init__( self, file ):
self.file = file
self.current_chrom = None
self.current_pos = -1
self.current_step = -1
self.current_span = -1
self.mode = MODE_BED
def __iter__( self ):
return self
def __next__( self ):
while True:
line = self.file.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
elif line.startswith( "variableStep" ):
header = parse_header( line )
self.current_chrom = header['chrom']
self.current_pos = -1
self.current_step = -1
if 'span' in header:
self.current_span = int( header['span'] )
else:
self.current_span = 1
self.mode = MODE_VARIABLE
continue
elif line.startswith( "fixedStep" ):
header = parse_header( line )
self.current_chrom = header['chrom']
self.current_pos = int( header['start'] ) - 1
self.current_step = int( header['step'] )
if 'span' in header:
self.current_span = int( header['span'] )
else:
self.current_span = 1
self.mode = MODE_FIXED
continue
elif self.mode == MODE_BED:
fields = line.split()
if len( fields ) > 3:
if len( fields ) > 5:
return fields[0], int( fields[1] ), int( fields[2] ), fields[5], float( fields[3] )
else:
return fields[0], int( fields[1] ), int( fields[2] ), "+", float( fields[3] )
elif self.mode == MODE_VARIABLE:
fields = line.split()
try:
pos = int( fields[0] ) - 1
val = float( fields[1] )
except ValueError:
continue
return self.current_chrom, pos, pos + self.current_span, "+", val
elif self.mode == MODE_FIXED:
fields = line.split()
try:
val = float( fields[0] )
except ValueError:
continue
return self.current_chrom, self.current_pos, self.current_pos + self.current_span, "+", val
# FIXME: unreachable! need to test this and fix!
self.current_pos += self.current_step
else:
raise "Unexpected input line: %s" % line.strip()
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