def reverse_complement_to_longest_reading_frame(seq_iter,
gap_characters=['-'],
table=1,
allow_partial=True,
require_start_after_stop=True,
log_frequency=0):
for i, s in enumerate(remove_gaps(seq_iter,
gap_characters=gap_characters)):
if (log_frequency > 0) and (((i + 1) % log_frequency) == 0):
_LOG.info('{0}: Checking reverse complement of seq {1}...'.format(
datetime.datetime.now(), (i + 1)))
rc = sequtils.get_reverse_complement(s)
p1 = sequtils.get_longest_reading_frames(
seq_record=s,
table=table,
allow_partial=allow_partial,
require_start_after_stop=require_start_after_stop)
p2 = sequtils.get_longest_reading_frames(
seq_record=rc,
table=table,
allow_partial=allow_partial,
require_start_after_stop=require_start_after_stop)
_LOG.debug('{0}: read length {1}, rev comp read length {2}'.format(
s.id, len(p1[0].seq), len(p2[0].seq)))
if len(p2) == 0:
yield s
elif len(p1) == 0:
_LOG.warning('Reverse complementing sequence {0!r}'.format(rc.id))
yield rc
elif len(p2[0].seq) > len(p1[0].seq):
_LOG.warning('Reverse complementing sequence {0!r}'.format(rc.id))
yield rc
else:
yield s
def reverse_complement_to_longest_reading_frame(seq_iter,
gap_characters=['-'],
table = 1,
allow_partial = True,
require_start_after_stop = True,
log_frequency = 0):
for i, s in enumerate(remove_gaps(seq_iter, gap_characters=gap_characters)):
if (log_frequency > 0) and (((i + 1) % log_frequency) == 0):
_LOG.info('{0}: Checking reverse complement of seq {1}...'.format(
datetime.datetime.now(),
(i + 1)))
rc = sequtils.get_reverse_complement(s)
p1 = sequtils.get_longest_reading_frames(seq_record = s,
table = table,
allow_partial = allow_partial,
require_start_after_stop = require_start_after_stop)
p2 = sequtils.get_longest_reading_frames(seq_record = rc,
table = table,
allow_partial = allow_partial,
require_start_after_stop = require_start_after_stop)
_LOG.debug('{0}: read length {1}, rev comp read length {2}'.format(
s.id, len(p1[0].seq), len(p2[0].seq)))
if len(p2) == 0:
yield s
elif len(p1) == 0:
_LOG.warning('Reverse complementing sequence {0!r}'.format(rc.id))
yield rc
elif len(p2[0].seq) > len(p1[0].seq):
_LOG.warning('Reverse complementing sequence {0!r}'.format(rc.id))
yield rc
else:
yield s
def summarize_longest_read_lengths(seq_iter,
gap_characters=['-'],
table=1,
allow_partial=True,
require_start_after_stop=True):
lengths = []
for seq in seqmod.remove_gaps(seq_iter, gap_characters=gap_characters):
l = 0
rcl = 0
lrf = sequtils.get_longest_reading_frames(
seq,
table=table,
allow_partial=allow_partial,
require_start_after_stop=require_start_after_stop)
if lrf:
l = len(lrf[0].seq)
rc_lrf = sequtils.get_longest_reading_frames(
sequtils.get_reverse_complement(seq),
table=table,
allow_partial=allow_partial,
require_start_after_stop=require_start_after_stop)
if rc_lrf:
rcl = len(rc_lrf[0].seq)
lengths.append((l, rcl, seq.id))
return sorted(lengths)
def summarize_longest_read_lengths(seq_iter,
gap_characters=['-'],
table = 1,
allow_partial = True,
require_start_after_stop = True):
lengths = []
for seq in seqmod.remove_gaps(seq_iter,
gap_characters = gap_characters):
l = 0
rcl = 0
lrf = sequtils.get_longest_reading_frames(
seq,
table = table,
allow_partial = allow_partial,
require_start_after_stop = require_start_after_stop)
if lrf:
l = len(lrf[0].seq)
rc_lrf = sequtils.get_longest_reading_frames(
sequtils.get_reverse_complement(seq),
table = table,
allow_partial = allow_partial,
require_start_after_stop = require_start_after_stop)
if rc_lrf:
rcl = len(rc_lrf[0].seq)
lengths.append((l, rcl, seq.id))
return sorted(lengths)
def test_require_start_after_stop(self):
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA',
IUPAC.ambiguous_dna),
id='1')
exp = SeqRecord(Seq('ATGACCAACTGA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(
seq, table=1, allow_partial=True, require_start_after_stop=True)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertFalse(lrf is seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA',
IUPAC.ambiguous_dna),
id='1')
exp = SeqRecord(Seq('ATGACCAACTGA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(
seq, table=1, allow_partial=False, require_start_after_stop=True)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertFalse(lrf is seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA',
IUPAC.ambiguous_dna),
id='1')
exp = SeqRecord(Seq('ATAGAAATTGGCCATGACCAACTGAATA',
IUPAC.ambiguous_dna),
id='1')
lrf = sequtils.get_longest_reading_frames(
seq, table=1, allow_partial=True, require_start_after_stop=False)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertFalse(lrf is seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA',
IUPAC.ambiguous_dna),
id='1')
exp = SeqRecord(Seq('ATGACCAACTGA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(
seq, table=1, allow_partial=False, require_start_after_stop=False)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertFalse(lrf is seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
def test_require_start_after_stop(self):
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA', IUPAC.ambiguous_dna), id='1')
exp = SeqRecord(Seq('ATGACCAACTGA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(seq,
table = 1,
allow_partial = True,
require_start_after_stop = True)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertNotEqual(lrf, seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA', IUPAC.ambiguous_dna), id='1')
exp = SeqRecord(Seq('ATGACCAACTGA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(seq,
table = 1,
allow_partial = False,
require_start_after_stop = True)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertNotEqual(lrf, seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA', IUPAC.ambiguous_dna), id='1')
exp = SeqRecord(Seq('ATAGAAATTGGCCATGACCAACTGAATA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(seq,
table = 1,
allow_partial = True,
require_start_after_stop = False)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertNotEqual(lrf, seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
seq = SeqRecord(Seq('TAGATAGATAGAAATTGGCCATGACCAACTGAATA', IUPAC.ambiguous_dna), id='1')
exp = SeqRecord(Seq('ATGACCAACTGA', IUPAC.ambiguous_dna), id='1')
lrf = sequtils.get_longest_reading_frames(seq,
table = 1,
allow_partial = False,
require_start_after_stop = False)
self.assertEqual(len(lrf), 1)
lrf = lrf[0]
self.assertNotEqual(lrf, seq)
self.assertSameMetadata(lrf, seq)
self.assertEqual(str(lrf.seq), str(exp.seq))
def longest_reading_frames(seq_iter,
gap_characters=['-'],
table = 1,
allow_partial = True,
require_start_after_stop = True):
for i, s in enumerate(remove_gaps(seq_iter, gap_characters=gap_characters)):
lrf = sequtils.get_longest_reading_frames(s,
table = table,
allow_partial = allow_partial,
require_start_after_stop = require_start_after_stop)
if lrf:
yield lrf[0]
else:
yield sequtils.copy_seq_metadata(s, '')
def longest_reading_frames(seq_iter,
gap_characters=['-'],
table=1,
allow_partial=True,
require_start_after_stop=True):
for i, s in enumerate(remove_gaps(seq_iter,
gap_characters=gap_characters)):
lrf = sequtils.get_longest_reading_frames(
s,
table=table,
allow_partial=allow_partial,
require_start_after_stop=require_start_after_stop)
if lrf:
yield lrf[0]
else:
yield sequtils.copy_seq_metadata(s, '')