def unique_contiguous_region_filter(sequence):
'''It filters out the snv in regions repeated in the genome or
discontiguous'''
if sequence is None:
return None
for snv in sequence.get_features(kind='snv'):
# Check if it is already done
previous_result = _get_filter_result(snv, 'uniq_contiguous',
threshold=distance)
if previous_result is not None:
continue
#we make a blast
#with the sequence around the snv
location = snv.location.start.position
start = location - distance
end = location + distance
if start < 0:
start = 0
#print start, end
seq_fragment = sequence[start:end]
blast_fhand = blast_runner(seq_fragment)['blastn']
#now we parse the blast
blast_result = blast_parser(blast_fhand)
alignments = filter_alignments(blast_result, config=match_filters)
#are there any similar sequences?
try:
alignment = alignments.next()
result = True
except StopIteration:
#if there is no similar sequence we assume that is unique
result = False
if result:
#how many matches, it should be only one
num_hits = len(alignment['matches'])
if num_hits > 1:
result = True
else:
#how many match parts have the first match?
#we could do it with the blast result, but blast is not very
#good aligning, so we realign with est2genome
blast_fhand.seek(0)
sim_seqs = similar_sequences_for_blast(blast_fhand)
sim_seq = sim_seqs[0] if sim_seqs else None
introns = infer_introns_for_cdna(sequence=seq_fragment,
genomic_seqs_index=genomic_seqs_index,
similar_sequence=sim_seq,
genomic_db=genomic_db)
if introns:
result = True
else:
result = False
blast_fhand.close()
_add_filter_result(snv, 'uniq_contiguous', result, distance)
return sequence
def annotate_intron(sequence):
'It adds the orf to the SeqFeatures'
if sequence is None:
return
try:
introns = infer_introns_for_cdna(sequence=sequence,
genomic_db=genomic_db,
genomic_seqs_index=genomic_seqs_index)
except KeyError as error:
error = str(error).lstrip('u').strip("'")
if 'not found' in error:
error += ' in seq file %s, but present in blast db %s' % \
(genomic_seqs_fhand.name, genomic_db)
raise RuntimeError(error)
for intron_pos in introns:
feature = SeqFeature(location=FeatureLocation(intron_pos,
intron_pos),
type='intron',
qualifiers={'genomic_db':genomic_db})
sequence.features.append(feature)
return sequence
def test_infer_introns_est2genome_method():
'It tests the est2genome method of infering introns'
seq = 'GAAAAGATGTGATTGGTGAAATAAGTTTGCCTCAATTCTCTTGTGCCGAAGTTCCAAAGAAGC'
seq += 'AGTTGGTGAATGAGCAGCCAGTACCCGAAAAATCGAGCAAAGATTTTGTGATGTATGTTGGAG'
seq += 'GTCTAGCATGGGGGATGGACTGGTGTCCCCAAGCTCATGAAAATAGGGATGCTCCTATGAAAA'
seq += 'GTGAGTTTGTCGCAATTGCTCCTCATCCTCCTGATTCATCATATCACAAGACTGATGCCTCAC'
seq += 'TTACAGGCAGAGGTGTAATTCAGATATGGTGCCTGCCAGATCTCATTCAAAAAGATATAATTG'
seq += 'TGAAAGAAGATTATTTTGCTCAGGTTAACAAAAAACCGTATAGAAATTTGACAAGAAGTGAAG'
seq += 'CAGGTACGGGAGAAGTATCTGGACCTCAAAAACCAAGAGGAAGACCAAAAAAGAACCCTGGTA'
seq += 'AAGCAGTCCAGGCAAAAGCATCTAGACCACAAAATCCAAGAGGAAGACCGAGAAAGAAGCCTG'
seq += 'TTACTGAATCTTTAGGTGATAGAGATAGTGAAGACCACAGTTTACAACCTCTTGCTATAGAGT'
seq += 'GGTCGCTGCAATCAACAGAACTTTCTGTAGATTTGTCTTGTGGAAATATGAATAAAGCCCAAG'
seq += 'TAGATATTGCGCTGAGTCAAGAAAGATGTATTAATGCGGCAT'
seq1 = SeqWithQuality(seq = Seq(seq))
tomato_genome = 'tomato_genome2+'
genomic_db = os.path.join(TEST_DATA_DIR, 'blast', tomato_genome)
genomic_seqs_index = SeqIO.index(genomic_db, 'fasta')
introns = infer_introns_for_cdna(seq1, genomic_db,
genomic_seqs_index=genomic_seqs_index)
assert introns == [478, 572, 613]
