def test_no_protein_support(self):
"""Testing no protein support for embl"""
# TODO: add protein support
# a fake protein line.
handle = io.StringIO('ID M14399; SV 1; linear; mRNA; STD; '
'PRO; 63 AA.\n//\n')
with self.assertRaisesRegex(EMBLFormatError,
r"There's no protein support for EMBL "
"record"):
# read a protein record
Protein.read(handle)
# return to 0
handle.seek(0)
with self.assertRaisesRegex(EMBLFormatError,
r"There's no protein support for EMBL "
"record"):
# read a generic record
skbio.io.read(handle, format='embl')
def test_no_protein_support(self):
"""Testing no protein support for embl"""
# TODO: add protein support
# a fake protein line.
handle = io.StringIO('ID M14399; SV 1; linear; mRNA; STD; '
'PRO; 63 AA.\n//\n')
with self.assertRaisesRegex(
EMBLFormatError, r"There's no protein support for EMBL "
"record"):
# read a protein record
Protein.read(handle)
# return to 0
handle.seek(0)
with self.assertRaisesRegex(
EMBLFormatError, r"There's no protein support for EMBL "
"record"):
# read a generic record
skbio.io.read(handle, format='embl')
def mask_sequence(hhsuite_fp,
fullsequence_fp,
subsequences_fp=None,
min_prob=None,
max_pvalue=None,
max_evalue=None,
min_fragment_length=0,
min_identity=0):
""" Splits a protein sequence according to HHsuits results.
The returned sub-sequences will seamlessly build the full sequence if
re-concatenated.
Parameters
----------
hhsuite_fp : str
Filepath to HHblits/HHsearch output.
fullsequence_fp : str
Filepath to the protein sequence of the original query.
subsequences_fp : str
Filepath to which sub-sequences are written as a multiple fasta file.
Each sequence makes up one header and one sequence file, i.e. sequences
are not wrapped.
Two files will be produced, suffixed by '.match' and '.non_match'. The
first holds sub-sequences of hits, the second holds the none-hit
covered subsequences.
Default: None, i.e. no file is written.
min_prob: float
Minimal probability of a hit to be included in the resulting list.
Note: probabilities are in the range of 100.0 to 0.0.
Default: None, i.e. no filtering on probability.
max_pvalue: float
Maximal P-value of a hit to be included in the resulting list.
Default: None, i.e. no filtering on P-value.
max_evalue: float
Maximal E-value of a hit to be included in the resulting list.
Default: None, i.e. no filtering on E-value.
min_fragment_length: int
Minimal fragment length of a hit to be included in the resulting list.
Default: 0, i.e. no filtering on fragment length.
min_identity: float
Minimum pair-wise sequence identity of a hit to be included in the
resulting list.
Default: 0, i.e. no filtering on sequence identity.
Returns
-------
[(str, str)] where first component is a fasta header, while the second is
its fasta sequence.
Raises
------
IOError
If the file cannot be written.
Notes
-----
A hit must satisfy ALL filtering options (min_prob, max_pvalue, max_evalue,
min_fragment_length) to be included in the resulting list.
"""
# parse hits from file
hits = parse_pdb_match(hhsuite_fp)
# filter hits
if min_prob is not None:
hits = [hit for hit in hits if hit['Probab'] >= min_prob]
if max_pvalue is not None:
hits = [hit for hit in hits if hit['P-value'] <= max_pvalue]
if max_evalue is not None:
hits = [hit for hit in hits if hit['E-value'] <= max_evalue]
if min_fragment_length is not None:
hits = [hit for hit in hits if frag_size(hit) >= min_fragment_length]
if min_identity is not None:
hits = [hit for hit in hits if hit['Identities'] >= min_identity]
# read the original protein file, used to run HHsearch
p = Protein.read(fullsequence_fp, seq_num=1)
query_id = p.metadata['id']
query_desc = p.metadata['description']
results = {'match': [], 'non_match': []}
# select non overlapping positive hits
subseqs_pos = select_hits(hits, e_value_threshold=999999)
for hit in subseqs_pos:
_id = get_q_id(hit)
match_id = hit['Hit'].split()[0]
header = "%s %s %s" % (correct_header_positions(
query_id, hit['alignment'][_id]['start'],
hit['alignment'][_id]['end']), '# %s' % match_id, query_desc)
seq = hit['alignment'][_id]['sequence'].replace('-', '')
results['match'].append((header, seq, hit['alignment'][_id]['start']))
# collect gaps between positive hits
subseqs_neg = report_uncovered_subsequences(subseqs_pos, str(p),
min_fragment_length)
for hit in subseqs_neg:
header = "%s %s" % (correct_header_positions(query_id, hit['start'],
hit['end']), query_desc)
seq = hit['sequence']
results['non_match'].append((header, seq, hit['start']))
# write sub-sequences to a multiple fasta file, sequences are un-wrapped
try:
# sort by start position
for type_ in results:
results[type_] = sorted(results[type_], key=lambda x: x[2])
if subsequences_fp is not None:
for type_ in results:
f = open('%s.%s' % (subsequences_fp, type_), 'w')
for res in results[type_]:
f.write(">%s\n%s\n" % res[:2])
f.close()
# removing the start position component from all subsequences
return {
type_: list(map(lambda x: x[:2], results[type_]))
for type_ in results
}
except IOError:
raise IOError('Cannot write to file "%s"' % subsequences_fp)
def mask_sequence(hhsuite_fp, fullsequence_fp, subsequences_fp=None,
min_prob=None, max_pvalue=None, max_evalue=None,
min_fragment_length=0):
""" Splits a protein sequence according to HHsuits results.
The returned sub-sequences will seamlessly build the full sequence if
re-concatenated.
Parameters
----------
hhsuite_fp : str
Filepath to HHblits/HHsearch output.
fullsequence_fp : str
Filepath to the protein sequence of the original query.
subsequences_fp : str
Filepath to which sub-sequences are written as a multiple fasta file.
Each sequence makes up one header and one sequence file, i.e. sequences
are not wrapped.
Two files will be produced, suffixed by '.match' and '.non_match'. The
first holds sub-sequences of hits, the second holds the none-hit
covered subsequences.
Default: None, i.e. no file is written.
min_prob: float
Minimal probability of a hit to be included in the resulting list.
Note: probabilities are in the range of 100.0 to 0.0.
Default: None, i.e. no filtering on probability.
max_pvalue: float
Maximal P-value of a hit to be included in the resulting list.
Default: None, i.e. no filtering on P-value.
max_evalue: float
Maximal E-value of a hit to be included in the resulting list.
Default: None, i.e. no filtering on E-value.
min_fragment_length: int
Minimal fragment length of a hit to be included in the resulting list.
Default: 0, i.e. no filtering on fragment length.
Returns
-------
[(str, str)] where first component is a fasta header, while the second is
its fasta sequence.
Raises
------
IOError
If the file cannot be written.
Notes
-----
A hit must satisfy ALL filtering options (min_prob, max_pvalue, max_evalue,
min_fragment_length) to be included in the resulting list.
"""
# parse hits from file
hits = parse_pdb_match(hhsuite_fp)
# filter hits
if min_prob is not None:
hits = [hit for hit in hits if hit['Probab'] >= min_prob]
if max_pvalue is not None:
hits = [hit for hit in hits if hit['P-value'] <= max_pvalue]
if max_evalue is not None:
hits = [hit for hit in hits if hit['E-value'] <= max_evalue]
if min_fragment_length is not None:
hits = [hit for hit in hits if frag_size(hit) >= min_fragment_length]
# read the original protein file, used to run HHsearch
p = Protein.read(fullsequence_fp, seq_num=1)
query_id = p.metadata['id']
query_desc = p.metadata['description']
results = {'match': [], 'non_match': []}
# select non overlapping positive hits
subseqs_pos = select_hits(hits, e_value_threshold=999999)
for hit in subseqs_pos:
_id = get_q_id(hit)
match_id = hit['Hit'].split()[0]
header = "%s %s %s" % (correct_header_positions(
query_id,
hit['alignment'][_id]['start'],
hit['alignment'][_id]['end']), '# %s' % match_id, query_desc)
seq = hit['alignment'][_id]['sequence'].replace('-', '')
results['match'].append((header, seq, hit['alignment'][_id]['start']))
# collect gaps between positive hits
subseqs_neg = report_uncovered_subsequences(subseqs_pos, str(p),
min_fragment_length)
for hit in subseqs_neg:
header = "%s %s" % (correct_header_positions(
query_id,
hit['start'],
hit['end']), query_desc)
seq = hit['sequence']
results['non_match'].append((header, seq, hit['start']))
# write sub-sequences to a multiple fasta file, sequences are un-wrapped
try:
# sort by start position
for type_ in results:
results[type_] = sorted(results[type_], key=lambda x: x[2])
if subsequences_fp is not None:
for type_ in results:
f = open('%s.%s' % (subsequences_fp, type_), 'w')
for res in results[type_]:
f.write(">%s\n%s\n" % res[:2])
f.close()
# removing the start position component from all subsequences
return {type_: list(map(lambda x: x[:2], results[type_]))
for type_ in results}
except IOError:
raise IOError('Cannot write to file "%s"' % subsequences_fp)
