def test_uclust_search_and_align_from_fasta_filepath(self):
""" uclust_search_and_align_from_fasta_filepath functions as expected """
# rev comp matches allowed (default)
actual = list(uclust_search_and_align_from_fasta_filepath(
self.search_align_query1_fp,self.search_align_template1_fp))
self.assertEqual(actual,self.search_align_out1_expected)
# rev comp matches not allowed
actual = list(uclust_search_and_align_from_fasta_filepath(
self.search_align_query1_fp,self.search_align_template1_fp,
enable_rev_strand_matching=False))
self.assertEqual(actual,self.search_align_out1_expected[:2])
def test_uclust_search_and_align_from_fasta_filepath_protein(self):
""" uclust_search_and_align_from_fasta_filepath functions with protein """
# rev comp matches allowed (default)
actual = list(
uclust_search_and_align_from_fasta_filepath(self.search_align_query2_fp, self.search_align_template2_fp)
)
self.assertEqual(actual, self.search_align_out2_expected)
def ipynast_seqs(candidate_sequences, template_alignment,
max_hits=30, min_pct=75.0, min_len=1000, align_unaligned_seqs_f=None,
log_fp=None, logger=None,**kwargs):
"""Iterator that yields results of pynast on candidate_sequences
This function yields the sequence and exit status of the alignment step,
as (sequence, exit status) tuples.
Status values can be:
0 : indicates a sucessful alignment, in which case the sequence will be
aligned
1 : indicates unsucessful sequence search, in which case the sequence
will be unaligned
2 : indicates alignment did not meet minimum requirements, in which case
the sequence will be unaligned
All sequences are returned as DNA sequence objects.
candidate_sequences
an iterable object (e.g., a list) containing tuples of
(seq_id, sequence) pairs (e.g., as returned by MinimalFastaParser)
or a fasta filepath
template_alignment
a PyCogent alignment object containing the template alignment
or a fasta filepath
max_hits
Maximum number of uclust hits to return
min_pct
minimum % identity for best database match
min_len
minimum length of match for alignment
align_unaligned_seqs_f
Function to align sequences. Must be of the form:
align_unaligned_seqs(seqs, moltype, params=None)
see cogent.app.muscle_v38.align_unaligned_seqs
log_fp
Optional path to log file
logger
Optional NastLogger object, takes precedence over log_fp
"""
deprecation_warning(kwargs)
files_to_remove = []
if type(candidate_sequences) == str:
# filepath provided for candidate sequences
candidate_sequences = MinimalFastaParser(open(candidate_sequences))
# sequence list provided for candidate sequence -- write
# the seqs to a temp file to pass to uclust. This is done in all
# cases to convert the sequences to uppercase in case they're not already.
# The bad handling of upper versus lower-cased sequences is a uclust issue.
candidate_fasta_filepath = \
get_tmp_filename(prefix='pynast_candidate',suffix='.fasta')
candidate_fasta_f = open(candidate_fasta_filepath,'w')
for seq_id, seq in candidate_sequences:
candidate_fasta_f.write('>%s\n%s\n' % (seq_id,str(seq).upper()))
candidate_fasta_f.close()
files_to_remove.append(candidate_fasta_filepath)
# degap the template alignment for the sequence searching step and
# write it to file
template_fasta_filepath = \
get_tmp_filename(prefix='pynast_template',suffix='.fasta')
template_fasta_f = open(template_fasta_filepath,'w')
if type(template_alignment) == str:
# the template alignment was received as a filepath
try:
template_alignment_f = open(template_alignment)
except IOError:
raise IOError,\
"Cannot open specified filepath: %s" % template_alignment
# template alignment provided as filepath -- process it iteratively
# to handle potentially massive template_alignments
template_alignment = {}
for seq_id,seq in MinimalFastaParser(template_alignment_f):
template_alignment[seq_id] = seq
seq = Sequence(seq=seq,moltype=DNA)
template_fasta_f.write('>%s\n%s\n' % (seq_id,seq.degap()))
else:
# the template alignment was received as a filepath
template_fasta_f.write(template_alignment.degap().toFasta())
template_fasta_f.close()
files_to_remove.append(template_fasta_filepath)
# Set up logging. NastLogger object takes precedence over log
# file path, if both are provided.
if logger is not None:
logger = logger
elif log_fp is not None:
logger = NastLogger(log_fp)
else:
logger = NastLogger()
min_pct /= 100.
# get the alignment iterator
pw_alignment_iterator = uclust_search_and_align_from_fasta_filepath(
candidate_fasta_filepath,
template_fasta_filepath,
percent_ID=min_pct,
enable_rev_strand_matching=True)
try:
current_result = pw_alignment_iterator.next()
except StopIteration:
current_result = None
for seq_id, seq in MinimalFastaParser(open(candidate_fasta_filepath)):
seq_len = len(seq)
if '-' in seq:
# clean-up temporary blast database files if any were created
pw_alignment_iterator.close()
remove_files(files_to_remove,error_on_missing=False)
raise ValueError, "Candidate sequence contains gaps. This is not supported."
try:
candidate_seq_id, template_seq_id, pw_aligned_candidate,\
pw_aligned_template, pct_identity = current_result
except TypeError:
pass
if not current_result or seq_id.split()[0] != candidate_seq_id.split()[0]:
# a suitable match was not found - don't align the sequence
# log the failure
logger.record(
seq_id, # input sequence identifier
len(seq), # input sequence length
"No search results.")
# yield the unaligned sequence and failure code
yield DNA.makeSequence(seq,Name=seq_id), 1
else:
# this sequence was aligned
if align_unaligned_seqs_f:
# if an alternate pairwise aligner was specified, unalign
# and re-align the sequences.
pw_aligned_template, pw_aligned_candidate =\
align_two_seqs(pw_aligned_template.replace('-',''),
pw_aligned_candidate.replace('-',''),
align_unaligned_seqs_f)
# Cast the pairwise alignments to DNA sequence objects
pw_aligned_candidate = \
DNA.makeSequence(pw_aligned_candidate,Name=candidate_seq_id)
pw_aligned_template = \
DNA.makeSequence(pw_aligned_template,Name=template_seq_id)
# Remove any terminal gaps that were introduced into the template
# sequence
pw_aligned_candidate, pw_aligned_template = \
remove_template_terminal_gaps(
pw_aligned_candidate, pw_aligned_template)
candidate_seq_id = pw_aligned_candidate.Name
# get the aligned template sequence from the template alignment
try:
template_aligned_seq = \
template_alignment.getGappedSeq(template_seq_id)
except AttributeError:
template_aligned_seq = \
Sequence(seq=template_alignment[template_seq_id],moltype=DNA)
# reintroduce the gap spacing from the template alignment
pw_aligned_template, pw_aligned_candidate, new_gaps =\
reintroduce_template_spacing(template_aligned_seq,\
pw_aligned_template,pw_aligned_candidate)
# delete any new gaps that were introduced during the
# pairwise alignment step
pw_aligned_template, pw_aligned_candidate = adjust_alignment(\
pw_aligned_template,pw_aligned_candidate,new_gaps)
# reintroduce any terminal gaps that were present in the template
result = introduce_terminal_gaps(\
template_aligned_seq,pw_aligned_template,pw_aligned_candidate)
unaligned_length = len(result.degap())
if unaligned_length < min_len:
# alignment is too short - log this as a failure
error = "Alignment does not meet minimum length "+\
"requirement for alignment (%d < %d)"\
% (seq_len,min_len)
logger.record(
seq_id, # input sequence identifier
len(seq), # input sequence length
"No search results.")
# yield the unaligned sequence and failure code
yield DNA.makeSequence(seq,Name=seq_id), 2
else:
# log the alignment
logger.record(
seq_id, # input sequence identifier
len(seq), # input sequence length
'', # Errors
template_seq_id, # best template match id
'%3.2f' % pct_identity, # pct id to template
unaligned_length, # post alignment sequence length
)
# yield the aligned sequence and sucess code
yield DNA.makeSequence(result,Name=candidate_seq_id), 0
# get the next alignment
try:
current_result = pw_alignment_iterator.next()
except StopIteration:
# end of the input fasta file indicates completion,
# not end of the aligned sequences
continue
# clean-up temporary blast database files if any were created
remove_files(files_to_remove,error_on_missing=False)
def test_uclust_search_and_align_from_fasta_filepath_protein(self):
""" uclust_search_and_align_from_fasta_filepath functions with protein """
# rev comp matches allowed (default)
actual = list(uclust_search_and_align_from_fasta_filepath(
self.search_align_query2_fp,self.search_align_template2_fp))
self.assertEqual(actual,self.search_align_out2_expected)
