def test_get_seqs():
seqname = '1'
args = parse_args((os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
seq = get_seq(args, seqname)
print str(seq)
assert str(seq) == 'CCCACACCGCGCAAAATTCTATACCAAAATCGACCT'
args = parse_args(('--translate', os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
seq = get_seq(args, seqname, start=2)
print str(seq)
assert str(seq) == 'PHRAKFYTKID'
def test_parse_args():
args = parse_args((os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
assert args.blastfilename == os.path.join(test_dir, 'test.tblastn')
assert args.seqfilename == os.path.join(test_dir, 'test.fa')
assert args.column_names == 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'
assert args.evalue == 10
assert args.index_filename == os.path.join(test_dir, 'test.inx')
assert args.program == 'tblastn'
assert args.subject_name == 'test'
assert args.translate is False
args = parse_args(('--translate', os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
assert args.translate
args = parse_args(('--translate', '--evalue', '1e-20', os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
assert args.evalue == 1e-20
def test_parse_blast():
"""Putting it all together"""
args = parse_args(('--translate', os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
seqs = parse_blast(args)
assert len(seqs) == 11
print seqs[0].seq[:30]
assert seqs[0].seq.find("RSQTPNSSVADDTRLHKRSMTISKGHSVSVVLISAALETIAASKEARRSTVIRESTQK") == 0
print seqs[0].seq.count('*')
assert seqs[0].seq.count('*') == 13
print len(seqs[0].seq)
assert len(seqs[0].seq) == 1809
args = parse_args(('--translate', '--evalue', '1e-70', os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
seqs = parse_blast(args)
assert len(seqs) == 1
print seqs[0].seq[:30]
assert seqs[0].seq.find("RSQTPNSSVADDTRLHKRSMTISKGHSVSVVLISAALETIAASKEARRSTVIRESTQK") == 0
print seqs[0].seq.count('*')
assert seqs[0].seq.count('*') == 13
print len(seqs[0].seq)
assert len(seqs[0].seq) == 1809
def test_combine_hits():
"""this will ensure that all pairs of coordinates are in the correct order (lowest to
highest for + strand hits; highest to lowest for - strand hits"""
args = parse_args((os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa')))
results = top_query(args)
for result in results:
coords = combine_hits(result)
print coords
if coords[0][0] < coords[0][1]:
for x in range(len(coords)-1):
assert coords[x][0] > coords[x+1][0]
else:
for x in range(len(coords)-1):
assert coords[x][0] < coords[x+1][0]
def test_top_query(): #I can add to this to test the evalue filtering args = parse_args((os.path.join(test_dir, 'test.tblastn'), os.path.join(test_dir, 'test.fa'))) results = top_query(args) assert len(results) == 11 assert len(results[0]) == 12 assert results[0][0]['pident'] == 61.77
