def test_build_water_relations():
'''it test the function that makes the relations between two sequences
using a markx10 format file'''
seq = 'ATGGCTTCATCCATTCTCTCATCCGCCGNTGTGGCCTTTGNCAACAGGGCTTCCCCTGCTCA'
seq += 'AGCTAGCATGGGGGCACCATTCACTGGCCTAAAATCCGCCGCTGCTTTCCCNGTTTTATGTA'
seq += 'CTGTTTTNACTCGCANGACCAACGACATCACCACTTTGGTTAGCAATGGGGGAAGAGTTCAG'
seq += 'GGCNTGAAGGTGTGCCCACCACTTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCTGA'
seq += 'TATGAGTAACGAGCAATTGGGAAAGGAAGTTGACTACCTTCTCAGGAAGGGATGGATTCCCT'
seq += 'GCATTGAATTCGACATTCACAGTGGATTCGTTTACCGTGAGACCCACAGGTCACCAGGATAC'
seq += 'TTCGATGGACGCTACTGGACCATGTGGAAGCTGCCCATGTTTGGCTGCACCGAT'
seq2 = 'ATGGCTTCATCCATTCTCTCATCCGCCGNTGTGGCCTTTGNCAACAGGGCTTCCCTGCTCAA'
seq2 += 'GCTAGCATGGGGGCACCATTCACTGGCCTAAAATCCGCCGCTGCTTTCCCNGTNACTCGCAN'
seq2 += 'GACCAACGACATCACCACTTTGGTTAGCAATGGGGGAAGAGTTCAGGGCNTGAAGGTGTGCC'
seq2 += 'CACCACTTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCTGATATGAGTAACGAGCAA'
seq2 += 'TTGGGAAAGGAAGTTGACTACCTTCTCAGGAAGGGATGGATTCCCTGCATTGAATTCGACAT'
seq2 += 'TCACAGTGGATTCGTTTACCGTGAGACCCACAGGTCACCAGGATACTTCGATGGACGCTAC'
seq2 += 'TGGACCATGTGGAAGCTGCCCATGTTTGGCTGCACCGAT'
subject_seq = SeqWithQuality(seq=Seq(seq), name='subject')
query_seq = SeqWithQuality(seq=Seq(seq2), name='query')
subject_fhand = temp_fasta_file(subject_seq)
parameters = {'subject':subject_fhand.name}
aligner = create_runner(tool='water', parameters=parameters)
result_fhand = aligner(query_seq)['water']
relations = build_relations_from_aligment(result_fhand,
query_name=query_seq.name,
subject_name=subject_seq.name)
assert relations == {'query': [(0, 50), (51, 112), (113, 409)],
'subject': [(0, 50), (52, 113), (129, 425)]}
def _locate_codons_in_orf(sequence, orf, snv):
'It locates the snv in the orf coordinate system'
query_name = sequence.name
orf_seq = orf.qualifiers['dna']
subject_name = 'subject'
subject_fhand = NamedTemporaryFile(suffix='.fasta')
subject_fhand.write('>%s\n%s\n' % (subject_name, orf_seq))
subject_fhand.flush()
parameters = {'subject':subject_fhand.name}
aligner = create_runner(tool='water', parameters=parameters)
result_fhand = aligner(sequence)['water']
relations = build_relations_from_aligment(result_fhand,
query_name=sequence.name,
subject_name=subject_name)
#print relations
coord = CoordSystem(relations=[relations])
# snv .positions
snv_pos = snv.location.start.position
try:
snv_in_orf = coord.transform(from_mol=query_name, to_mol=subject_name,
position=snv_pos)
except RuntimeError:
snv_in_orf = None
#print snv_in_orf_start, snv_in_orf_end
orf_start = 0
orf_end = len(orf.qualifiers['dna']) - 1
orf_start_limit_in_seq = coord.transform(from_mol=subject_name,
to_mol=query_name,
position=orf_start)
orf_end_limit_in_seq = coord.transform(from_mol=subject_name,
to_mol=query_name,
position=orf_end)
if snv_in_orf is None:
# it can be utr3, utr5, or None
if snv_pos < orf_start_limit_in_seq:
position = 'utr5'
elif snv_pos > orf_end_limit_in_seq:
position = 'in utr3'
else:
position = None
codon_start = None
snv_in_orf = None
else:
start_codon_pos = snv_in_orf % 3
codon_start = snv_in_orf - start_codon_pos
position = 'orf'
return (position, codon_start, snv_in_orf)