block_sizes = tokens[10].split(',')
block_starts = tokens[11].split(',')
# Handle trailing commas
try:
int(block_sizes[-1])
except ValueError:
block_sizes = block_sizes[:-1]
try:
int(block_starts[-1])
except ValueError:
block_starts = block_starts[:-1]
block_count = len(block_sizes)
assert block_count == len(block_starts)
true_seq = ''.join([reference_index.get_stretch(
chrom,
chrom_start + int(block_starts[i]),
int(block_sizes[i])
) for i in xrange(block_count)]).upper()
if tokens[5] == '-':
true_seq = true_seq[::-1].translate(
_reversed_complement_translation_table
)
for i in xrange(args.length):
truths[i] += 1
if true_seq[i] == seq[i]:
recalls[i] += 1
k += 1
overall_truths = sum(truths)
overall_recalls = sum(recalls)
print 'Read count: %d' % read_count
print 'Overall error rate: %.12f' % (
for i in xrange(1, len(exons_from_transcript)):
if exons_from_transcript[i][0] == exons_from_transcript[i-1][0]:
# Kill any introns 4 bases or smaller
if (exons_from_transcript[i][1]
- exons_from_transcript[i-1][2]) < 5:
continue
intron = (exons_from_transcript[i][0],
exons_from_transcript[i-1][2] + 1,
exons_from_transcript[i][1] - 1)
print '\t'.join((intron[0], str(intron[1]), str(intron[2])))
introns.add(intron)
if args.bowtie2_idx is not None:
for intron in introns:
length = intron[2] - intron[1] + 1
motif = (reference_index.get_stretch(intron[0],
intron[1] - 1,
2),
reference_index.get_stretch(intron[0],
intron[1]
+ length - 3,
2))
intron_lengths[length] += 1
motif_counts[motif] += 1
for length, frequency in sorted(intron_lengths.items()):
print >>sys.stderr, '%d\t%d' % (length, frequency)
all_motifs = set([('GT', 'AG'), ('GC', 'AG'), ('AT', 'AC'),
('CT', 'AC'), ('CT', 'GC'), ('GT', 'AT')])
canonicals = set([('GT', 'AG'), ('CT', 'AC')])
less_canonicals = set([('GC', 'AG'), ('CT', 'GC')])
much_less_canonicals = set([('AT', 'AC'), ('GT', 'AT')])
canonical = 0
# Recall that GTF is end-inclusive, and so is STAR's junctions.txt
for i in xrange(1, len(exons_from_transcript)):
if exons_from_transcript[i][0] == exons_from_transcript[i - 1][0]:
# Kill any introns 4 bases or smaller
if (exons_from_transcript[i][1] -
exons_from_transcript[i - 1][2]) < 5:
continue
intron = (exons_from_transcript[i][0],
exons_from_transcript[i - 1][2] + 1,
exons_from_transcript[i][1] - 1)
print '\t'.join((intron[0], str(intron[1]), str(intron[2])))
introns.add(intron)
if args.bowtie2_idx is not None:
for intron in introns:
length = intron[2] - intron[1] + 1
motif = (reference_index.get_stretch(intron[0], intron[1] - 1, 2),
reference_index.get_stretch(intron[0],
intron[1] + length - 3, 2))
intron_lengths[length] += 1
motif_counts[motif] += 1
for length, frequency in sorted(intron_lengths.items()):
print >> sys.stderr, '%d\t%d' % (length, frequency)
all_motifs = set([('GT', 'AG'), ('GC', 'AG'), ('AT', 'AC'),
('CT', 'AC'), ('CT', 'GC'), ('GT', 'AT')])
canonicals = set([('GT', 'AG'), ('CT', 'AC')])
less_canonicals = set([('GC', 'AG'), ('CT', 'GC')])
much_less_canonicals = set([('AT', 'AC'), ('GT', 'AT')])
canonical = 0
less_canonical = 0
much_less_canonical = 0
one_off_other = 0
block_sizes = tokens[10].split(',')
block_starts = tokens[11].split(',')
# Handle trailing commas
try:
int(block_sizes[-1])
except ValueError:
block_sizes = block_sizes[:-1]
try:
int(block_starts[-1])
except ValueError:
block_starts = block_starts[:-1]
block_count = len(block_sizes)
assert block_count == len(block_starts)
true_seq = ''.join([
reference_index.get_stretch(
chrom, chrom_start + int(block_starts[i]),
int(block_sizes[i])) for i in xrange(block_count)
]).upper()
if tokens[5] == '-':
true_seq = true_seq[::-1].translate(
_reversed_complement_translation_table)
for i in xrange(args.length):
truths[i] += 1
if true_seq[i] == seq[i]:
recalls[i] += 1
k += 1
overall_truths = sum(truths)
overall_recalls = sum(recalls)
print 'Read count: %d' % read_count
print 'Overall error rate: %.12f' % (
float(overall_truths - overall_recalls) / overall_truths)
