def test_deblur_with_non_default_error_profile(self):
error_dist = [
1, 0.05, 0.000005, 0.000005, 0.000005, 0.000005, 0.0000025,
0.0000025, 0.0000025, 0.0000025, 0.0000025, 0.0000005, 0.0000005,
0.0000005, 0.0000005
]
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(parse_fasta(seqs_f), error_dist=error_dist)
exp = [
Sequence(
"E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")
]
# Trying with a numpy array
error_dist = np.array([
1, 0.05, 0.000005, 0.000005, 0.000005, 0.000005, 0.0000025,
0.0000025, 0.0000025, 0.0000025, 0.0000025, 0.0000005, 0.0000005,
0.0000005, 0.0000005
])
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(parse_fasta(seqs_f), error_dist=error_dist)
self.assertEqual(obs, exp)
def test_deblur_with_non_default_error_profile(self):
error_dist = [
1,
0.05,
0.000005,
0.000005,
0.000005,
0.000005,
0.0000025,
0.0000025,
0.0000025,
0.0000025,
0.0000025,
0.0000005,
0.0000005,
0.0000005,
0.0000005,
]
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(parse_fasta(seqs_f), error_dist=error_dist)
exp = [
Sequence(
"E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag",
)
]
# Trying with a numpy array
error_dist = np.array(
[
1,
0.05,
0.000005,
0.000005,
0.000005,
0.000005,
0.0000025,
0.0000025,
0.0000025,
0.0000025,
0.0000025,
0.0000005,
0.0000005,
0.0000005,
0.0000005,
]
)
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(parse_fasta(seqs_f), error_dist=error_dist)
self.assertEqual(obs, exp)
def test_deblur_indel(self):
"""Test if also removes indel sequences
"""
seqs_f = StringIO(TEST_SEQS_2)
# add the MSA for the indel
seqs = sequence_generator(seqs_f)
newseqs = []
for chead, cseq in seqs:
tseq = cseq[:10] + '-' + cseq[10:]
newseqs.append((chead, tseq))
# now add a sequence with an A insertion
tseq = cseq[:10] + 'A' + cseq[10:-1] + '-'
newseqs.append((chead, tseq))
obs = deblur(newseqs)
# remove the '-' (same as in launch_workflow)
for s in obs:
s.sequence = s.sequence.replace('-', '')
# the expected output
exp = [
Sequence(
"E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")
]
# make sure we get 1 sequence as output
self.assertEqual(len(obs), 1)
# and that it is the correct sequence
self.assertEqual(obs[0].sequence, exp[0].sequence)
def test_deblur(self):
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(parse_fasta(seqs_f))
exp = [
Sequence("E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")]
self.assertEqual(obs, exp)
def test_deblur_toy_example(self):
seqs_f = StringIO(TEST_SEQS_1)
obs = deblur(sequence_generator(seqs_f))
exp = [
Sequence(
"E.Coli;size=1000;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")
]
self.assertEqual(obs, exp)
def test_deblur(self):
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(parse_fasta(seqs_f))
exp = [
Sequence(
"E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag",
)
]
self.assertEqual(obs, exp)
def test_deblur_indel(self):
"""Test if also removes indel sequences
"""
seqs_f = StringIO(TEST_SEQS_2)
# add the MSA for the indel
seqs = sequence_generator(seqs_f)
newseqs = []
for chead, cseq in seqs:
tseq = cseq[:10] + '-' + cseq[10:]
newseqs.append((chead, tseq))
# now add a sequence with an A insertion at the expected freq. (30 < 0.02 * (720 / 0.47) where 0.47 is the mod_factor) so should be removed
cseq = newseqs[0][1]
tseq = cseq[:10] + 'A' + cseq[11:-1] + '-'
chead = '>indel1-read;size=30;'
newseqs.append((chead, tseq))
# and add a sequence with an A insertion but at higher freq. (not expected by indel upper bound - (31 > 0.02 * (720 / 0.47) so should not be removed)
cseq = newseqs[0][1]
tseq = cseq[:10] + 'A' + cseq[11:-1] + '-'
chead = '>indel2-read;size=31;'
newseqs.append((chead, tseq))
obs = deblur(newseqs)
# remove the '-' (same as in launch_workflow)
for s in obs:
s.sequence = s.sequence.replace('-', '')
# the expected output
exp = [
Sequence(
"E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")
]
# make sure we get 2 sequences as output - the original and the indel2 (too many reads for the expected indel probabilty)
self.assertEqual(len(obs), 2)
# and that it is the correct sequence
self.assertEqual(obs[0].sequence, exp[0].sequence)
self.assertEqual(obs[1].label, '>indel2-read;size=31;')
def launch_workflow(seqs_fp,
working_dir,
mean_error,
error_dist,
indel_prob,
indel_max,
trim_length,
left_trim_length,
min_size,
ref_fp,
ref_db_fp,
threads_per_sample=1,
sim_thresh=None,
coverage_thresh=None):
"""Launch full deblur workflow for a single post split-libraries fasta file
Parameters
----------
seqs_fp: string
a post split library fasta file for debluring
working_dir: string
working directory path
mean_error: float
mean error for original sequence estimate
error_dist: list
list of error probabilities for each hamming distance
indel_prob: float
insertion/deletion (indel) probability
indel_max: integer
maximal indel number
trim_length: integer
sequence trim length
left_trim_length: integer
trim the first n reads
min_size: integer
upper limit on sequence abundance (discard sequences below limit)
ref_fp: tuple
filepath(s) to FASTA reference database for artifact removal
ref_db_fp: tuple
filepath(s) to SortMeRNA indexed database for artifact removal
threads_per_sample: integer, optional
number of threads to use for SortMeRNA/mafft/vsearch
(0 for max available)
sim_thresh: float, optional
the minimal similarity for a sequence to the database.
if None, take the defaults (0.65 for negate=False,
0.95 for negate=True)
coverage_thresh: float, optional
the minimal coverage for alignment of a sequence to the database.
if None, take the defaults (0.3 for negate=False, 0.95 for negate=True)
Return
------
output_no_chimers_fp : string
filepath to fasta file with no chimeras of None if error encountered
"""
logger = logging.getLogger(__name__)
logger.info('--------------------------------------------------------')
logger.info('launch_workflow for file %s' % seqs_fp)
# Step 1: Trim sequences to specified length
output_trim_fp = join(working_dir, "%s.trim" % basename(seqs_fp))
with open(output_trim_fp, 'w') as out_f:
for label, seq in trim_seqs(input_seqs=sequence_generator(seqs_fp),
trim_len=trim_length,
left_trim_len=left_trim_length):
out_f.write(">%s\n%s\n" % (label, seq))
# Step 2: Dereplicate sequences
output_derep_fp = join(working_dir, "%s.derep" % basename(output_trim_fp))
dereplicate_seqs(seqs_fp=output_trim_fp,
output_fp=output_derep_fp,
min_size=min_size,
threads=threads_per_sample)
# Step 3: Remove artifacts
output_artif_fp, num_seqs_left, _ = remove_artifacts_seqs(
seqs_fp=output_derep_fp,
ref_fp=ref_fp,
working_dir=working_dir,
ref_db_fp=ref_db_fp,
negate=True,
threads=threads_per_sample,
sim_thresh=sim_thresh)
if not output_artif_fp:
warnings.warn('Problem removing artifacts from file %s' % seqs_fp,
UserWarning)
logger.warning('remove artifacts failed, aborting')
return None
# Step 4: Multiple sequence alignment
if num_seqs_left > 1:
output_msa_fp = join(working_dir, "%s.msa" % basename(output_artif_fp))
alignment = multiple_sequence_alignment(seqs_fp=output_artif_fp,
threads=threads_per_sample)
if not alignment:
warnings.warn(
'Problem performing multiple sequence alignment '
'on file %s' % seqs_fp, UserWarning)
logger.warning('msa failed. aborting')
return None
elif num_seqs_left == 1:
# only one sequence after remove artifacts (but could be many reads)
# no need to run MSA - just use the pre-msa file as input for next step
output_msa_fp = output_artif_fp
else:
err_msg = ('No sequences left after artifact removal in '
'file %s' % seqs_fp)
warnings.warn(err_msg, UserWarning)
logger.warning(err_msg)
return None
# Step 5: Launch deblur
output_deblur_fp = join(working_dir, "%s.deblur" % basename(output_msa_fp))
with open(output_deblur_fp, 'w') as f:
seqs = deblur(sequence_generator(output_msa_fp), mean_error,
error_dist, indel_prob, indel_max)
if seqs is None:
warnings.warn(
'multiple sequence alignment file %s contains '
'no sequences' % output_msa_fp, UserWarning)
logger.warn('no sequences returned from deblur for file %s' %
output_msa_fp)
return None
for s in seqs:
# remove '-' from aligned sequences
s.sequence = s.sequence.replace('-', '')
f.write(s.to_fasta())
# Step 6: Chimera removal
output_no_chimeras_fp = remove_chimeras_denovo_from_seqs(
output_deblur_fp, working_dir, threads=threads_per_sample)
logger.info('finished processing file')
return output_no_chimeras_fp
def test_deblur_noseqs(self):
"""If no sequences supplied, need to return None
"""
res = deblur([])
self.assertEqual(res, None)
def launch_workflow(seqs_fp,
working_dir,
read_error,
mean_error,
error_dist,
indel_prob,
indel_max,
trim_length,
min_size,
ref_fp,
ref_db_fp,
negate,
threads=1,
delim='_'):
"""Launch full deblur workflow.
Parameters
----------
seqs_fp: string
post split library sequences for debluring
working_dir: string
working directory path
read_error: float
read error rate
mean_error: float
mean error for original sequence estimate
error_dist: list
list of error probabilities for each hamming distance
indel_prob: float
insertion/deletion (indel) probability
indel_max: integer
maximal indel number
trim_length: integer
sequence trim length
min_size: integer
upper limit on sequence abundance (discard sequences below limit)
ref_fp: tuple
filepath(s) to FASTA reference database for artifact removal
ref_db_fp: tuple
filepath(s) to SortMeRNA indexed database for artifact removal
negate: boolean
discard all sequences aligning to the ref_fp database
threads: integer, optional
number of threads to use for SortMeRNA
delim: string, optional
delimiter in FASTA labels to separate sample ID from sequence ID
Return
------
biom_fp: string
filepath to BIOM table
"""
# Step 1: Trim sequences to specified length
output_trim_fp = join(working_dir, "%s.trim" % basename(seqs_fp))
with open(seqs_fp, 'U') as in_f, open(output_trim_fp, 'w') as out_f:
for label, seq in trim_seqs(input_seqs=parse_fasta(in_f),
trim_len=trim_length):
out_f.write(">%s\n%s\n" % (label, seq))
# Step 2: Dereplicate sequences
output_derep_fp = join(working_dir, "%s.derep" % basename(output_trim_fp))
dereplicate_seqs(seqs_fp=output_trim_fp,
output_fp=output_derep_fp,
min_size=min_size,
uc_output=True)
# Step 3: Remove artifacts
output_artif_fp = remove_artifacts_seqs(seqs_fp=output_derep_fp,
ref_fp=ref_fp,
working_dir=working_dir,
ref_db_fp=ref_db_fp,
negate=negate,
threads=threads)
# Step 4: Multiple sequence alignment
output_msa_fp = join(working_dir, "%s.msa" % basename(output_artif_fp))
with open(output_msa_fp, 'w') as f:
alignment = multiple_sequence_alignment(seqs_fp=output_artif_fp,
threads=threads)
f.write(alignment.to_fasta())
# Step 5: Launch deblur
output_deblur_fp = join(working_dir, "%s.deblur" % basename(output_msa_fp))
with open(output_deblur_fp, 'w') as f:
seqs = deblur(parse_fasta(output_msa_fp), read_error, mean_error,
error_dist, indel_prob, indel_max)
for s in seqs:
# remove '-' from aligned sequences
s.sequence = s.sequence.replace('-', '')
f.write(s.to_fasta())
# Step 6: Chimera removal
output_no_chimeras_fp = remove_chimeras_denovo_from_seqs(
output_deblur_fp, working_dir)
# Step 7: Generate BIOM table
deblur_clrs, table = generate_biom_table(seqs_fp=output_no_chimeras_fp,
uc_fp="%s.uc" % output_trim_fp,
delim=delim)
# Step 8: Write BIOM table to file
if table.is_empty():
raise ValueError("Attempting to write an empty BIOM table.")
biom_fp = join(working_dir, "%s.biom" % basename(seqs_fp))
write_biom_table(table, biom_fp)
return biom_fp
def launch_workflow(
seqs_fp,
output_fp,
read_error,
mean_error,
error_dist,
indel_prob,
indel_max,
trim_length,
min_size,
ref_fp,
ref_db_fp,
negate,
threads,
delim,
):
"""Launch full deblur workflow.
Parameters
----------
seqs_fp: string
post split library sequences for debluring
output_fp: string
filepath to output file
read_error: float
read error rate
mean_error: float
mean error for original sequence estimate
error_dist: list
list of error probabilities for each hamming distance
indel_prob: float
insertion/deletion (indel) probability
indel_max: integer
maximal indel number
trim_length: integer
sequence trim length
min_size: integer
upper limit on sequence abundance (discard sequences below limit)
ref_fp: tuple
filepath(s) to FASTA reference database for artifact removal
ref_db_fp: tuple
filepath(s) to SortMeRNA indexed database for artifact removal
negate: boolean
discard all sequences aligning to the ref_fp database
threads: integer
number of threads to use for SortMeRNA
delim: string
delimiter in FASTA labels to separate sample ID from sequence ID
"""
# Step 1: Trim sequences to specified length
output_trim_fp = join(dirname(output_fp), "%s.trim" % basename(seqs_fp))
with open(seqs_fp, "U") as in_f, open(output_trim_fp, "w") as out_f:
for label, seq in trim_seqs(input_seqs=parse_fasta(in_f), trim_len=trim_length):
out_f.write(">%s\n%s\n" % (label, seq))
# Step 2: Dereplicate sequences
output_derep_fp = join(dirname(output_fp), "%s.derep" % basename(output_trim_fp))
dereplicate_seqs(seqs_fp=output_trim_fp, output_fp=output_derep_fp, min_size=min_size, uc_output=True)
# Step 3: Remove artifacts
output_artif_fp = join(dirname(output_fp), "%s.no_artifacts" % basename(output_derep_fp))
remove_artifacts_seqs(
seqs_fp=output_derep_fp,
ref_fp=ref_fp,
output_fp=output_artif_fp,
ref_db_fp=ref_db_fp,
negate=negate,
threads=threads,
)
# Step 4: Multiple sequence alignment
output_msa_fp = join(dirname(output_fp), "%s.msa" % basename(output_artif_fp))
with open(output_msa_fp, "w") as f:
alignment = multiple_sequence_alignment(output_artif_fp)
f.write(alignment.to_fasta())
# Step 5: Launch deblur
output_deblur_fp = join(dirname(output_fp), "%s.deblur" % basename(output_msa_fp))
with open(output_deblur_fp, "w") as f:
seqs = deblur(parse_fasta(output_msa_fp), read_error, mean_error, error_dist, indel_prob, indel_max)
for s in seqs:
# remove '-' from aligned sequences
s.sequence = s.sequence.replace("-", "")
f.write(s.to_fasta())
# Step 6: Chimera removal
output_no_chimeras_fp = join(dirname(output_fp), "%s.no_chimeras" % basename(output_deblur_fp))
remove_chimeras_denovo_from_seqs(output_deblur_fp, output_no_chimeras_fp)
# Step 7: Generate BIOM table
deblur_clrs, table = generate_biom_table(seqs_fp=output_no_chimeras_fp, uc_fp="%s.uc" % output_trim_fp, delim=delim)
# Step 8: Write BIOM table to file
if table.is_empty():
raise ValueError("Attempting to write an empty BIOM table.")
with biom_open(output_fp, "w") as f:
if HAVE_H5PY:
table.to_hdf5(h5grp=f, generated_by="deblur")
else:
table.to_json(direct_io=f, generated_by="deblur")
