def test_add_rg_to_bam(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
lib_name = 'aa'
log_fhand = NamedTemporaryFile()
readgroup = {
'ID': lib_name,
'PL': 'illumina',
'LB': lib_name,
'SM': '{0}_illumina_pe'.format(lib_name),
'PU': '0'
}
bwa = map_with_bwamem(index_fpath,
unpaired_fpath=reads_fpath,
readgroup=readgroup,
log_fpath=log_fhand.name)
map_process_to_bam(bwa, bam_fhand.name)
out = subprocess.check_output(
[get_binary_path('samtools'), 'view', '-h', bam_fhand.name],
stderr=log_fhand)
assert '@RG\tID:aa' in out
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
directory.close()
def test_tophat(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath, directory.name,
unpaired_fpath=reads_fpath)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
directory.close()
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bowtie2(index_fpath, bam_fhand.name,
unpaired_fpaths=[reads_fpath])
directory.close()
def test_tophat(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath,
directory.name,
unpaired_fpath=reads_fpath)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
directory.close()
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bowtie2(index_fpath,
bam_fhand.name,
unpaired_fpaths=[reads_fpath])
directory.close()
def test_map_with_bwa(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bwasw(index_fpath, bam_fhand.name, unpaired_fpath=reads_fpath)
out = subprocess.check_output([get_binary_path('samtools'), 'view',
bam_fhand.name])
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
directory.close()
def test_map_with_bwa(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
map_with_bwasw(index_fpath, bam_fhand.name, unpaired_fpath=reads_fpath)
out = subprocess.check_output(
[get_binary_path('samtools'), 'view', bam_fhand.name])
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
directory.close()
def test_plot_window(self):
iterator = itertools.chain(self.gen_windows(),
self.gen_windows('ch2'))
tempdir = TemporaryDir()
out_base = join(tempdir.name, 'out')
labels = OrderedDict({'val1': {'title': 'val1 title',
'ylabel': 'val1 ylabel'},
'val2': {'title': 'val2 title',
'ylabel': 'val2 ylabel'}})
plot_in_genome(iterator, out_base=out_base, labels=labels)
# raw_input(tempdir.name)
tempdir.close()
def test_plot_window(self):
iterator = itertools.chain(self.gen_windows(),
self.gen_windows('ch2'))
tempdir = TemporaryDir()
out_base = join(tempdir.name, 'out')
labels = OrderedDict({'val1': {'title': 'val1 title',
'ylabel': 'val1 ylabel'},
'val2': {'title': 'val2 title',
'ylabel': 'val2 ylabel'}})
plot_in_genome(iterator, out_base=out_base, labels=labels)
# raw_input(tempdir.name)
tempdir.close()
def test_plot_window(self):
iterator = itertools.chain(self.gen_windows(), self.gen_windows("ch2"))
tempdir = TemporaryDir()
out_base = join(tempdir.name, "out")
labels = OrderedDict(
{
"val1": {"title": "val1 title", "ylabel": "val1 ylabel"},
"val2": {"title": "val2 title", "ylabel": "val2 ylabel"},
}
)
plot_in_genome(iterator, out_base=out_base, labels=labels)
# raw_input(tempdir.name)
tempdir.close()
def test_tophat_paired(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_1_fpath = os.path.join(TEST_DATA_DIR, 'reads_1.fastq')
reads_2_fpath = os.path.join(TEST_DATA_DIR, 'reads_2.fastq')
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath,
directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath])
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
self.fail('runtimeError expected')
except RuntimeError:
pass
finally:
directory.close()
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath,
directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath],
mate_inner_dist=350,
mate_std_dev=50)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
finally:
directory.close()
def get_or_create_bwa_index(fpath, directory=None):
'It creates the bwa index for the given reference'
fpath = os.path.abspath(fpath)
if directory is not None:
index_fpath = os.path.join(directory, os.path.basename(fpath))
else:
index_fpath = fpath
if not _bwa_index_exists(index_fpath):
if os.path.exists(index_fpath):
temp_dir = TemporaryDir()
tmp_index_fpath = os.path.join(temp_dir.name,
os.path.basename(index_fpath))
os.symlink(fpath, tmp_index_fpath)
_create_bwa_index(tmp_index_fpath)
for file_ in os.listdir(temp_dir.name):
if file_ == os.path.basename(index_fpath):
continue
shutil.copy(os.path.join(temp_dir.name, file_),
os.path.join(os.path.dirname(index_fpath), file_))
else:
os.symlink(fpath, index_fpath)
_create_bwa_index(index_fpath)
return index_fpath
def test_blastdb():
'It creates a blast database.'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_path1 = get_or_create_blastdb(seq_fpath, directory=db_dir.name,
dbtype='nucl')
db_path = os.path.join(db_dir.name, db_name)
assert 'CATAGGGTCACCAATGGC' in open(db_path1).read(100)
assert db_path1 == db_path
assert os.path.exists(db_path)
index_fpath = os.path.join(db_dir.name, db_name + '.nsq')
assert os.path.exists(index_fpath)
finally:
db_dir.close()
def test_run_binary(self):
binary = join(VCF_BIN_DIR, 'annotate_snvs')
assert 'usage' in check_output([binary, '-h'])
config = '''[1]
[[CloseToSnv]]
distance = 60
max_maf_depth = 0.7
[2]
[[HighVariableRegion]]
max_variability = 0.05
window_in_bp = 101
ref_fpath = '{sample_fasta}'
[3]
[[CapEnzyme]]
all_enzymes = True
ref_fpath = '{sample_fasta}'
[4]
[[HeterozigoteInSamples]]
filter_id = 1
[5]
[[IsVariableDepthAnnotator]]
filter_id = 1
samples = ['pep']
[6]
[[LowComplexityRegionAnnotator]]
ref_fpath = '{sample_fasta}'
'''
config = config.format(sample_fasta=REF_FREEBAYES)
config_fhand = NamedTemporaryFile(suffix='.config')
config_fhand.write(config)
config_fhand.flush()
tmp_dir = TemporaryDir()
cmd = [
binary, FREEBAYES3_VCF_PATH, '-f', config_fhand.name, '-p',
tmp_dir.name
]
# raw_input(' '.join(cmd))
result = check_output(cmd)
tmp_dir.close()
# print result
assert 'cs60_0.70\t' in result
assert 'CAP=MmeI' in result
assert 'HIS1=True' in result
assert '\tPASS\t' in result
def test_get_or_create_index(self):
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
assert not _bwa_index_exists(seq_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(seq_fpath, directory.name)
expected_index = os.path.join(directory.name,
os.path.basename(db_name))
assert index_fpath == expected_index
assert _bwa_index_exists(index_fpath)
# already exists
index_fpath = get_or_create_bwa_index(seq_fpath, directory.name)
assert index_fpath == expected_index
assert _bwa_index_exists(index_fpath)
directory.close()
def test_get_or_create_index(self):
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
assert _bowtie2_index_exists(seq_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(seq_fpath, directory.name)
expected_index = os.path.join(directory.name,
os.path.basename(db_name))
assert index_fpath == expected_index
assert _bowtie2_index_exists(index_fpath)
# already exists
index_fpath = get_or_create_bowtie2_index(seq_fpath, directory.name)
assert index_fpath == expected_index
assert _bowtie2_index_exists(index_fpath)
directory.close()
def test_blastdb():
'It creates a blast database.'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_path1 = get_or_create_blastdb(seq_fpath,
directory=db_dir.name,
dbtype='nucl')
db_path = os.path.join(db_dir.name, db_name)
assert 'CATAGGGTCACCAATGGC' in open(db_path1).read(100)
assert db_path1 == db_path
assert os.path.exists(db_path)
index_fpath = os.path.join(db_dir.name, db_name + '.nsq')
assert os.path.exists(index_fpath)
finally:
db_dir.close()
def test_blast_search(self):
'It does a blast search'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_fpath = get_or_create_blastdb(seq_fpath, directory=db_dir.name,
dbtype='nucl')
query_fhand = NamedTemporaryFile()
query_fhand.write(open(seq_fpath).read(200))
query_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fpath, db_fpath, program='blastn',
out_fpath=out_fhand.name)
assert '</BlastOutput>' in open(out_fhand.name).read()
finally:
db_dir.close()
def test_run_binary(self):
binary = join(VCF_BIN_DIR, 'annotate_snvs')
assert 'usage' in check_output([binary, '-h'])
config = '''[1]
[[CloseToSnv]]
distance = 60
max_maf_depth = 0.7
[2]
[[HighVariableRegion]]
max_variability = 0.05
window_in_bp = 101
ref_fpath = '{sample_fasta}'
[3]
[[CapEnzyme]]
all_enzymes = True
ref_fpath = '{sample_fasta}'
[4]
[[HeterozigoteInSamples]]
filter_id = 1
[5]
[[IsVariableDepthAnnotator]]
filter_id = 1
samples = ['pep']
[6]
[[LowComplexityRegionAnnotator]]
ref_fpath = '{sample_fasta}'
'''
config = config.format(sample_fasta=REF_FREEBAYES)
config_fhand = NamedTemporaryFile(suffix='.config')
config_fhand.write(config)
config_fhand.flush()
tmp_dir = TemporaryDir()
cmd = [binary, FREEBAYES3_VCF_PATH, '-f', config_fhand.name,
'-p', tmp_dir.name]
# raw_input(' '.join(cmd))
result = check_output(cmd)
tmp_dir.close()
# print result
assert 'cs60_0.70\t' in result
assert 'CAP=MmeI' in result
assert 'HIS1=True' in result
assert '\tPASS\t' in result
def test_get_or_create_blastdb():
blastdb = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
directory = TemporaryDir()
assert not _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
new_blast_path = os.path.join(directory.name,
os.path.basename(blastdb))
assert _blastdb_exists(new_blast_path, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
assert _blastdb_exists(new_blast_path, NUCL)
directory.close()
# already exists
blastdb = os.path.join(TEST_DATA_DIR, 'blastdbs', 'arabidopsis_genes')
assert _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL)
assert _blastdb_exists(blastdb, NUCL)
def test_get_or_create_blastdb():
blastdb = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
directory = TemporaryDir()
assert not _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
new_blast_path = os.path.join(directory.name,
os.path.basename(blastdb))
assert _blastdb_exists(new_blast_path, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
assert _blastdb_exists(new_blast_path, NUCL)
directory.close()
# already exists
blastdb = os.path.join(TEST_DATA_DIR, 'blastdbs', 'arabidopsis_genes')
assert _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL)
assert _blastdb_exists(blastdb, NUCL)
def test_filter_by_bowtie2_bin():
filter_bin = os.path.join(BIN_DIR, 'filter_by_bowtie2')
assert 'usage' in check_output([filter_bin, '-h'])
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(TEST_DATA_DIR,
'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
for reads_fpath in [fastq_fpath, fasta_fpath]:
out_fhand = NamedTemporaryFile(suffix='.seqs')
filtered_fhand = NamedTemporaryFile(suffix='.seqs')
cmd = [filter_bin, '-i', index_fpath, '-o', out_fhand.name,
'-e', filtered_fhand.name, reads_fpath]
check_output(cmd)
assert 'no_arabi' in open(out_fhand.name).read()
assert 'read1' in open(filtered_fhand.name).read()
directory.close()
def test_add_rg_to_bam(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bwa_index(reference_fpath, directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
lib_name = 'aa'
log_fhand = NamedTemporaryFile()
readgroup = {'ID': lib_name, 'PL': 'illumina', 'LB': lib_name,
'SM': '{0}_illumina_pe'.format(lib_name), 'PU': '0'}
bwa = map_with_bwamem(index_fpath, unpaired_fpath=reads_fpath,
readgroup=readgroup, log_fpath=log_fhand.name)
map_process_to_bam(bwa, bam_fhand.name)
out = subprocess.check_output([get_binary_path('samtools'), 'view',
'-h', bam_fhand.name], stderr=log_fhand)
assert '@RG\tID:aa' in out
assert 'TTCTGATTCAATCTACTTCAAAGTTGGCTTTATCAATAAG' in out
directory.close()
def _look_for_blast_matches(self, seq_fpath, oligos, seqs_type):
'It looks for the oligos in the given sequence files'
# we need to keep the blast_fhands, because they're temp files and
# otherwise they might be removed
temp_dir = TemporaryDir()
dbpath = os.path.join(temp_dir.name, os.path.basename(seq_fpath))
seqio([open(seq_fpath)],
open(dbpath, 'w'),
out_format='fasta',
copy_if_same_format=False)
blasts, blast_fhand = _do_blast_2(dbpath,
oligos,
params=self.params,
program=self.program,
dbtype=seqs_type)
if self.filters is not None:
blasts = filter_alignments(blasts, config=self.filters)
# Which are the regions covered in each sequence?
indexed_match_parts = {}
for blast in blasts:
oligo = blast['query']
for match in blast['matches']:
read = match['subject']
if self.elongate_for_global:
elongate_match_parts_till_global(
match['match_parts'],
query_length=oligo['length'],
subject_length=read['length'],
align_completely=QUERY)
# match_parts = [m['match_parts'] for m in blast['matches']]
match_parts = match['match_parts']
try:
indexed_match_parts[read['name']].extend(match_parts)
except KeyError:
indexed_match_parts[read['name']] = match_parts
temp_dir.close()
blast_fhand.close()
return indexed_match_parts
def test_blast_search(self):
'It does a blast search'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_fpath = get_or_create_blastdb(seq_fpath,
directory=db_dir.name,
dbtype='nucl')
query_fhand = NamedTemporaryFile()
query_fhand.write(open(seq_fpath).read(200))
query_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fpath,
db_fpath,
program='blastn',
out_fpath=out_fhand.name)
assert '</BlastOutput>' in open(out_fhand.name).read()
finally:
db_dir.close()
def test_filter_by_bowtie2_bin():
filter_bin = os.path.join(BIN_DIR, 'filter_by_bowtie2')
assert 'usage' in check_output([filter_bin, '-h'])
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(
TEST_DATA_DIR, 'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
for reads_fpath in [fastq_fpath, fasta_fpath]:
out_fhand = NamedTemporaryFile(suffix='.seqs')
filtered_fhand = NamedTemporaryFile(suffix='.seqs')
cmd = [
filter_bin, '-i', index_fpath, '-o', out_fhand.name, '-e',
filtered_fhand.name, reads_fpath
]
check_output(cmd)
assert 'no_arabi' in open(out_fhand.name).read()
assert 'read1' in open(filtered_fhand.name).read()
directory.close()
def test_filter_by_bowtie2():
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(TEST_DATA_DIR,
'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
passed = ['no_arabi']
for preffered_classes in [[SEQITEM], [SEQRECORD]]:
for reads_fpath in [fastq_fpath, fasta_fpath]:
seq_packets = read_seq_packets([open(reads_fpath)],
prefered_seq_classes=preffered_classes)
filter_packets = seq_to_filterpackets(seq_packets)
filter_ = FilterBowtie2Match(index_fpath)
filter_packet = list(filter_packets)[0]
filter_packets = filter_(filter_packet)
assert _seqs_to_names(filter_packets[SEQS_PASSED]) == passed
assert _seqs_to_names(filter_packets[SEQS_FILTERED_OUT]) == [
'read1', 'read2', 'read3']
directory.close()
def _look_for_blast_matches(self, seq_fpath, oligos):
"It looks for the oligos in the given sequence files"
# we need to keep the blast_fhands, because they're temp files and
# otherwise they might be removed
temp_dir = TemporaryDir()
dbpath = os.path.join(temp_dir.name, os.path.basename(seq_fpath))
seqio([open(seq_fpath)], [open(dbpath, "w")], out_format="fasta", copy_if_same_format=False)
blasts, blast_fhand = _do_blast_2(dbpath, oligos, params=self.params, program=self.program)
if self.filters is not None:
blasts = filter_alignments(blasts, config=self.filters)
# Which are the regions covered in each sequence?
indexed_match_parts = {}
one_oligo = True if len(oligos) == 1 else False
for blast in blasts:
oligo = blast["query"]
for match in blast["matches"]:
read = match["subject"]
if self.elongate_for_global:
elongate_match_parts_till_global(
match["match_parts"],
query_length=oligo["length"],
subject_length=read["length"],
align_completely=QUERY,
)
# match_parts = [m['match_parts'] for m in blast['matches']]
match_parts = match["match_parts"]
if one_oligo:
indexed_match_parts[read["name"]] = match_parts
else:
try:
indexed_match_parts[read["name"]].extend(match_parts)
except KeyError:
indexed_match_parts[read["name"]] = match_parts
temp_dir.close()
blast_fhand.close()
return indexed_match_parts
def test_tophat_paired(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_1_fpath = os.path.join(TEST_DATA_DIR, 'reads_1.fastq')
reads_2_fpath = os.path.join(TEST_DATA_DIR, 'reads_2.fastq')
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath, directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath])
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
self.fail('runtimeError expected')
except RuntimeError:
pass
finally:
directory.close()
try:
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
map_with_tophat(index_fpath, directory.name,
paired_fpaths=[reads_1_fpath, reads_2_fpath],
mate_inner_dist=350, mate_std_dev=50)
os.path.exists(os.path.join(directory.name, 'accepted_hits.bam'))
finally:
directory.close()
def test_rel_symlink(self):
'It tests various cases of rel symlinks'
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, 'hola')
os.mkdir(hola)
caracola = os.path.join(tempdir.name, 'caracola')
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, 'fname')
open(fname, 'w')
caracola2 = os.path.join(tempdir.name, 'caracola2')
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, 'dir1', 'dir2')
os.makedirs(path2)
caracola3 = os.path.join(path2, 'caracola3')
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
def test_filter_by_bowtie2():
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(os.path.join(
TEST_DATA_DIR, 'arabidopsis_genes'),
directory=directory.name)
fastq_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
fasta_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fasta')
passed = ['no_arabi']
for preffered_classes in [[SEQITEM], [SEQRECORD]]:
for reads_fpath in [fastq_fpath, fasta_fpath]:
seq_packets = read_seq_packets(
[open(reads_fpath)],
prefered_seq_classes=preffered_classes)
filter_packets = seq_to_filterpackets(seq_packets)
filter_ = FilterBowtie2Match(index_fpath)
filter_packet = list(filter_packets)[0]
filter_packets = filter_(filter_packet)
assert _seqs_to_names(filter_packets[SEQS_PASSED]) == passed
assert _seqs_to_names(filter_packets[SEQS_FILTERED_OUT]) == [
'read1', 'read2', 'read3'
]
directory.close()
def test_rel_symlink(self):
"It tests various cases of rel symlinks"
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, "hola")
os.mkdir(hola)
caracola = os.path.join(tempdir.name, "caracola")
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, "fname")
open(fname, "w")
caracola2 = os.path.join(tempdir.name, "caracola2")
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, "dir1", "dir2")
os.makedirs(path2)
caracola3 = os.path.join(path2, "caracola3")
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
def test_rel_symlink(self):
'It tests various cases of rel symlinks'
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, 'hola')
os.mkdir(hola)
caracola = os.path.join(tempdir.name, 'caracola')
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, 'fname')
open(fname, 'w')
caracola2 = os.path.join(tempdir.name, 'caracola2')
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, 'dir1', 'dir2')
os.makedirs(path2)
caracola3 = os.path.join(path2, 'caracola3')
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
def _look_for_blast_matches(self, seq_fpath, oligos, seqs_type):
'It looks for the oligos in the given sequence files'
# we need to keep the blast_fhands, because they're temp files and
# otherwise they might be removed
temp_dir = TemporaryDir()
dbpath = os.path.join(temp_dir.name, os.path.basename(seq_fpath))
seqio([open(seq_fpath)], open(dbpath, 'w'), out_format='fasta',
copy_if_same_format=False)
blasts, blast_fhand = _do_blast_2(dbpath, oligos, params=self.params,
program=self.program,
dbtype=seqs_type)
if self.filters is not None:
blasts = filter_alignments(blasts, config=self.filters)
# Which are the regions covered in each sequence?
indexed_match_parts = {}
for blast in blasts:
oligo = blast['query']
for match in blast['matches']:
read = match['subject']
if self.elongate_for_global:
elongate_match_parts_till_global(match['match_parts'],
query_length=oligo['length'],
subject_length=read['length'],
align_completely=QUERY)
# match_parts = [m['match_parts'] for m in blast['matches']]
match_parts = match['match_parts']
try:
indexed_match_parts[read['name']].extend(match_parts)
except KeyError:
indexed_match_parts[read['name']] = match_parts
temp_dir.close()
blast_fhand.close()
return indexed_match_parts
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, unpaired_fpath=reads_fpath)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
# With paired_fpahts option
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
forward_fpath = os.path.join(TEST_DATA_DIR, 'arabreads_1.fastq')
reverse_fpath = os.path.join(TEST_DATA_DIR, 'arabreads_2.fastq')
paired_fpaths = (forward_fpath, reverse_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, paired_fpaths=paired_fpaths)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
def test_downgrade_read_edges_binary(self):
binary = os.path.join(BAM_BIN_DIR, 'downgrade_bam_edge_qual')
bam_fpath = os.path.join(TEST_DATA_DIR, 'sample_rev.bam')
with NamedTemporaryFile() as out_fhand:
cmd = [binary, '-o', out_fhand.name, bam_fpath]
check_call(cmd)
sam = AlignmentFile(out_fhand.name)
res = [0, 0]
read = sam.next()
assert list(read.query_qualities[:2]) == res
assert read.get_tag('dl') == '8)5B'
assert read.get_tag('dr') == '8?>>'
# check bam substitution
with TemporaryDir() as tmp_dir:
dirname = tmp_dir.name
shutil.copy(bam_fpath, dirname)
bam_fpath = os.path.join(dirname, os.path.basename(bam_fpath))
cmd = [binary, bam_fpath, '-t', '/home/peio/']
check_call(cmd)
sam = AlignmentFile(bam_fpath)
res = [0, 0]
read = sam.next()
assert list(read.query_qualities[:2]) == res
assert read.get_tag('dl') == '8)5B'
assert read.get_tag('dr') == '8?>>'
# we can not downgrade an already downgraded bam
try:
cmd = [binary, bam_fpath]
stderr_fhand = NamedTemporaryFile()
check_call(cmd, stderr=stderr_fhand)
self.fail('CalledProcessError expected')
except CalledProcessError:
stderr_fhand.flush()
msg = 'RuntimeError: Edge qualities already downgraded'
if msg not in open(stderr_fhand.name).read():
raise
def test_map_with_bowtie2(self):
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
reads_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, unpaired_fpath=reads_fpath)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
#With paired_fpahts option
reference_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
forward_fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_reads.fastq')
reverse_fpath = NamedTemporaryFile().name
paired_fpaths = (forward_fpath, reverse_fpath)
directory = TemporaryDir()
index_fpath = get_or_create_bowtie2_index(reference_fpath,
directory.name)
bam_fhand = NamedTemporaryFile(suffix='.bam')
bowtie2 = map_with_bowtie2(index_fpath, paired_fpaths=paired_fpaths)
map_process_to_bam(bowtie2, bam_fhand.name)
directory.close()
