def filter_by_similar_seqs(sequence):
if sequence is None:
return False
similar_seqs = look_for_similar_sequences(sequence, db, blast_program,
filters=filters)
if reverse:
return not len(similar_seqs) >= 1
else:
return len(similar_seqs) >= 1
def test_look_for_similar_seqs():
'It test if we can look for simialr seqs in a database'
seq = 'AATCACCGAGCTCAAGGGTATTCAGGTGAAGAAATTCTTTATTTGGCTCGATGTCGATGAGA'
seq += 'TCAAGGTCGATCTTCCACCTTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAGAAG'
seq += 'CTTGATATTGACCAGTTTAAGACTATACATTCTTGTCACGATAATGGTGTCTCTGGCTCTTG'
seq += 'TGGAGATTCATGGAAGAGTTTTCTCGAGGTAAAGATTAGATCTT'
seq1 = SeqWithQuality(seq=Seq(seq))
database = os.path.join(TEST_DATA_DIR, 'blast', 'arabidopsis_genes+')
similar_seqs = look_for_similar_sequences(seq1, database=database,
blast_program='blastn')
assert similar_seqs[0]['name'] == 'AT5G19860.1'
assert similar_seqs[0]['query_start'] == 1
assert similar_seqs[0]['subject_start'] == 323
