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 test_temp_fasta_file_seq_iter():
'It test temp_fasta_file'
seqrec1 = SeqWithQuality(seq=Seq('ATGATAGATAGATGF'), name='seq1')
seqrec2 = SeqWithQuality(seq=Seq('ATGATAGATAGA'), name='seq2')
seq_iter = iter([seqrec1, seqrec2])
fhand = temp_fasta_file(seq_iter)
content = open(fhand.name).read()
assert content == ">seq1\nATGATAGATAGATGF\n>seq2\nATGATAGATAGA\n"
def infer_introns_for_cdna(sequence, genomic_db, genomic_seqs_index=None, similar_sequence=None):
"It infers the intron location in the cdna using est2genome"
if not similar_sequence:
# first we want to know where is the most similar seq in the genomic_db
# this will speed up things
similar_seqs = look_for_similar_sequences(sequence, database=genomic_db, blast_program="blastn")
if not similar_seqs:
return []
similar_seq = similar_seqs[0]
else:
similar_seq = similar_sequence
start = similar_seq["subject_start"]
end = similar_seq["subject_end"]
try:
similar_seq = genomic_seqs_index[similar_seq["name"]]
except KeyError:
msg = "Sequence %s was not found" % similar_seq["name"]
raise KeyError(msg)
# now we run est2genome for this cdna
cdna_file = temp_fasta_file(seqs=[sequence])
similar_seq_file = temp_fasta_file(seqs=[similar_seq])
# we run est2genome
cmd = [
"est2genome",
cdna_file.name,
similar_seq_file.name,
"-sbegin2",
str(start),
"-send2",
str(end),
"-stdout",
"-auto",
]
stdout, stderr, retcode = call(cmd)
if retcode:
msg = "There was an error running est2genome: " + stderr
raise RuntimeError(msg)
# parse est2genome
result = est2genome_parser(stdout)
# get_introns_from parser_result
return result["cdna"]["introns"]
def infer_introns_for_cdna(sequence, genomic_db, genomic_seqs_index=None,
similar_sequence=None):
'It infers the intron location in the cdna using est2genome'
if not similar_sequence:
#first we want to know where is the most similar seq in the genomic_db
#this will speed up things
similar_seqs = look_for_similar_sequences(sequence, database=genomic_db,
blast_program='blastn')
if not similar_seqs:
return []
similar_seq = similar_seqs[0]
else:
similar_seq = similar_sequence
start = similar_seq['subject_start']
end = similar_seq['subject_end']
try:
similar_seq = genomic_seqs_index[similar_seq['name']]
except KeyError:
msg = 'Sequence %s was not found' % similar_seq['name']
raise KeyError(msg)
#now we run est2genome for this cdna
cdna_file = temp_fasta_file(seqs=[sequence])
similar_seq_file = temp_fasta_file(seqs=[similar_seq])
#we run est2genome
cmd = ['est2genome', cdna_file.name, similar_seq_file.name,
'-sbegin2', str(start), '-send2', str(end), '-stdout', '-auto']
stdout, stderr, retcode = call(cmd)
if retcode:
msg = 'There was an error running est2genome: ' + stderr
raise RuntimeError(msg)
#parse est2genome
result = est2genome_parser(stdout)
#get_introns_from parser_result
return result['cdna']['introns']
def _prepare_input_files(inputs, seqs):
'It prepares inputs taking into account the format'
for key, value in inputs.items():
files_format = value['files_format']
inputs[key]['fhands'] = []
inputs[key]['fpaths'] = []
seqs, seqs_qual = itertools.tee(seqs, 2)
for file_format in files_format:
if file_format == 'fasta':
fhand = temp_fasta_file(seqs=seqs)
elif file_format == 'qual':
fhand = temp_qual_file(seqs=seqs_qual)
inputs[key]['fhands'].append(fhand)
inputs[key]['fpaths'].append(fhand.name)
def _prepare_input_files(inputs, seqs):
"It prepares inputs taking into account the format"
for key, value in inputs.items():
files_format = value["files_format"]
inputs[key]["fhands"] = []
inputs[key]["fpaths"] = []
seqs, seqs_qual = itertools.tee(seqs, 2)
for file_format in files_format:
if file_format == "fasta":
fhand = temp_fasta_file(seqs=seqs)
elif file_format == "qual":
fhand = temp_qual_file(seqs=seqs_qual)
inputs[key]["fhands"].append(fhand)
inputs[key]["fpaths"].append(fhand.name)
def test_temp_fasta_file_one_seq():
'It test temp_fasta_file'
seqrec1 = SeqWithQuality(seq=Seq('ATGATAGATAGATGF'), name='seq1')
fhand = temp_fasta_file(seqrec1)
content = open(fhand.name).read()
assert content == ">seq1\nATGATAGATAGATGF\n"
def _seq_to_fasta_fhand(seq):
'Given a fhand or Seq object it returns a fhand'
if 'file' in seq.__class__.__name__.lower():
return seq
return temp_fasta_file(seqs=[seq])
def test_strip_adaptor_blast(self):
"It tests strip_vector_by_alignment with blastn-short"
vec1 = SeqWithQuality(name="vec1", seq=Seq("atcgatcgatagcatacgat"))
vec2 = SeqWithQuality(name="vec2", seq=Seq("atgcatcagatcgataaaga"))
fhand_vectors = temp_fasta_file([vec1, vec2])
seq_trimmer = create_seq_trim_and_masker()
strip_vector_by_alignment = create_adaptor_striper(fhand_vectors)
seq = "ATGCATCAGATGCATGCATGACTACGACTACGATCAGCATCAGCGATCAGCATCGATACGATC"
seq = Seq(seq)
seq2 = SeqWithQuality(name="seq1", seq=seq)
seq1 = SeqWithQuality(name=seq2.name, seq=vec1.seq + seq2.seq + vec2.seq, description="hola")
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
assert seq3.description == "hola"
fhand_vectors.seek(0)
seq1 = SeqWithQuality(name=seq2.name, seq=vec1.seq + vec2.seq + seq2.seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
# overlaping vectors
fhand_vectors.seek(0)
new_seq = vec1.seq[:-2] + vec2.seq + seq2.seq + vec2.seq
seq1 = SeqWithQuality(name=seq2.name, seq=new_seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
# Now only vectors
fhand_vectors.seek(0)
new_seq = vec1.seq + vec2.seq + vec2.seq
seq1 = SeqWithQuality(name=seq2.name, seq=new_seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert seq3 is None
# Now without vectors
fhand_vectors.seek(0)
seq1 = seq2
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
fhand_vectors.seek(0)
seq1 = SeqWithQuality(name=seq2.name, seq=vec1.seq[::-1] + vec2.seq + seq2.seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
seq = "ATGCATCAGATGCATGCATGACTACGACTACGATCAGCATCAGCGATCAGCATCGATACGATC"
seq = Seq(seq)
seq2 = SeqWithQuality(name="seq1", seq=seq)
# 'atcgatcgatagcatacgat atgcatcagatcgataaaga
seq = "atcgatcgatagcataGgat" + seq2.seq + "atgGatcagatcgataaaga"
seq1 = SeqWithQuality(name=seq2.name, seq=seq, description="hola")
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
long_adap = "atcgatcgatagcatacgatatcgatcgatagcatacgatatcgatcgatagcatacc"
vec1 = SeqWithQuality(name="vec1", seq=Seq(long_adap))
fhand_vectors = temp_fasta_file([vec1])
try:
create_adaptor_striper(fhand_vectors)
self.fail("ValueError expected")
except ValueError:
pass