def gen_output_lines(args, fin):
"""
Yield observation lines, given a filtered pileup file open for reading.
"""
# unpack some relevant arguments
reqambig = args.reqambig
fill = args.fill
errlow, errhigh = args.errlow, args.errhigh
low = 1 if args.low == 'drosophila' else args.low
high = args.high
# create some state maintained across input lines
filler = None
chrom_name = None
name_to_drosophila_length = dict(DGRP.g_chromosome_length_pairs)
# define the default line to write
default_obs = (0, 0, 0, 0)
# process the input file line by line
for line in fin:
srow = line.split()
if not srow:
continue
row = DGRP.filtered_pileup_row_to_typed(srow)
obs = DGRP.filtered_pileup_typed_to_obs(row)
name, pos, ref = row[:3]
if filler is None:
# set the chromosome name
chrom_name = name
# if appropriate, update the high value using the chrom name
if args.high == 'drosophila':
high = name_to_drosophila_length.get(name, None)
if high is None:
raise Exception('invalid fly chromosome: ' + name)
else:
high = args.high
# define the filler generator object
filler = iterfiller.FillerGenerator(low, high,
fill, errlow, errhigh, default_obs)
# check the chromosome name for consistency
if name != chrom_name:
raise Exception(
'conflicting chromosome '
'names: %s %s' % (name, chrom_name))
# check for reference nucleotide weirdness
if reqambig:
if not filler.check_bounds(pos):
if ref != 'N':
raise Exception(
'expected out of bounds reference nucleotides '
'to be N but found %s '
'at position %d of chrom %s' % (ref, pos, name))
# process lines emitted by the filler
for value in filler.fill(pos, obs):
yield '\t'.join(str(x) for x in value)
# process final lines emitted by the filler
for value in filler.finish():
yield '\t'.join(str(x) for x in value)
def gen_typed_rows(fin):
for line in fin:
srow = line.split()
if srow:
yield DGRP.filtered_pileup_row_to_typed(srow)
def gen_typed_rows(fin):
for line in fin:
srow = line.split()
if srow:
yield DGRP.filtered_pileup_row_to_typed(srow)
