def modify_alignment(focus_ali, target_seq_index, target_seq_id, region_start,
**kwargs):
"""
Apply pairwise identity filtering, fragment filtering, and exclusion
of columns with too many gaps to a sequence alignment. Also generates
files describing properties of the alignment such as frequency distributions,
conservation, and "old-style" alignment statistics files.
.. note::
assumes focus alignment (otherwise unprocessed) as input.
.. todo::
come up with something more clever to filter fragments than fixed width
(e.g. use 95% quantile of length distribution as reference point)
Parameters
----------
focus_ali : Alignment
Focus-mode input alignment
target_seq_index : int
Index of target sequence in alignment
target_seq_id : str
Identifier of target sequence (without range)
region_start : int
Index of first sequence position in target sequence
kwargs : See required arguments in source code
Returns
-------
outcfg : Dict
File products generated by the function:
* alignment_file
* statistics_file
* frequencies_file
* identities_file
* raw_focus_alignment_file
ali : Alignment
Final processed alignment
"""
check_required(kwargs, [
"prefix",
"seqid_filter",
"hhfilter",
"minimum_sequence_coverage",
"minimum_column_coverage",
"compute_num_effective_seqs",
"theta",
])
prefix = kwargs["prefix"]
create_prefix_folders(prefix)
focus_fasta_file = prefix + "_raw_focus.fasta"
outcfg = {
"alignment_file": prefix + ".a2m",
"statistics_file": prefix + "_alignment_statistics.csv",
"frequencies_file": prefix + "_frequencies.csv",
"identities_file": prefix + "_identities.csv",
"raw_focus_alignment_file": focus_fasta_file,
}
# swap target sequence to first position if it is not
# the first sequence in alignment;
# this is particularly important for hhfilter run
# because target sequence might otherwise be filtered out
if target_seq_index != 0:
indices = np.arange(0, len(focus_ali))
indices[0] = target_seq_index
indices[target_seq_index] = 0
target_seq_index = 0
focus_ali = focus_ali.select(sequences=indices)
with open(focus_fasta_file, "w") as f:
focus_ali.write(f, "fasta")
# apply pairwise identity filter (using hhfilter)
if kwargs["seqid_filter"] is not None:
filtered_file = prefix + "_filtered.a3m"
at.run_hhfilter(focus_fasta_file,
filtered_file,
threshold=kwargs["seqid_filter"],
columns="first",
binary=kwargs["hhfilter"])
with open(filtered_file) as f:
focus_ali = Alignment.from_file(f, "a3m")
# final FASTA alignment before applying A2M format modifications
filtered_fasta_file = prefix + "_raw_focus_filtered.fasta"
with open(filtered_fasta_file, "w") as f:
focus_ali.write(f, "fasta")
ali = focus_ali
# filter fragments
# come up with something more clever here than fixed width
# (e.g. use 95% quantile of length distribution as reference point)
min_cov = kwargs["minimum_sequence_coverage"]
if min_cov is not None:
if isinstance(min_cov, int):
min_cov /= 100
keep_seqs = (1 - ali.count("-", axis="seq")) >= min_cov
ali = ali.select(sequences=keep_seqs)
# Calculate frequencies, conservation and identity to query
# on final alignment (except for lowercase modification)
# Note: running hhfilter might cause a loss of the target seque
# if it is not the first sequence in the file! To be sure that
# nothing goes wrong, target_seq_index should always be 0.
describe_seq_identities(ali, target_seq_index=target_seq_index).to_csv(
outcfg["identities_file"], float_format="%.3f", index=False)
describe_frequencies(ali, region_start,
target_seq_index=target_seq_index).to_csv(
outcfg["frequencies_file"],
float_format="%.3f",
index=False)
coverage_stats = describe_coverage(ali, prefix, region_start,
kwargs["minimum_column_coverage"])
# keep list of uppercase sequence positions in alignment
pos_list = np.arange(region_start, region_start + ali.L, dtype="int32")
# Make columns with too many gaps lowercase
min_col_cov = kwargs["minimum_column_coverage"]
if min_col_cov is not None:
if isinstance(min_col_cov, int):
min_col_cov /= 100
lc_cols = ali.count(ali._match_gap, axis="pos") > 1 - min_col_cov
ali = ali.lowercase_columns(lc_cols)
# if we remove columns, we have to update list of positions
pos_list = pos_list[~lc_cols]
else:
lc_cols = None
# compute effective number of sequences
# (this is intended for cases where coupling stage is
# not run, but this number is wanted nonetheless)
if kwargs["compute_num_effective_seqs"]:
# make sure we only compute N_eff on the columns
# that would be used for model inference, dispose
# the rest
if lc_cols is None:
cut_ali = ali
else:
cut_ali = ali.select(columns=~lc_cols)
# compute sequence weights
cut_ali.set_weights(kwargs["theta"])
# N_eff := sum of all sequence weights
n_eff = float(cut_ali.weights.sum())
# patch into coverage statistics (N_eff column)
coverage_stats.loc[:, "N_eff"] = n_eff
else:
n_eff = None
# save coverage statistics to file
coverage_stats.to_csv(outcfg["statistics_file"],
float_format="%.3f",
index=False)
# store description of final sequence alignment in outcfg
# (note these parameters will be updated by couplings protocol)
outcfg.update({
"num_sites": len(pos_list),
"num_sequences": len(ali),
"effective_sequences": n_eff,
"region_start": region_start,
})
# create segment in outcfg
outcfg["segments"] = [
Segment("aa", target_seq_id, region_start, region_start + ali.L - 1,
pos_list).to_list()
]
with open(outcfg["alignment_file"], "w") as f:
ali.write(f, "fasta")
return outcfg, ali
def _make_hmmsearch_raw_fasta(alignment_result, prefix):
"""
HMMsearch results do not contain the query sequence
so we must construct a raw_fasta file with the query
sequence as the first hit, to ensure proper numbering.
The search result is filtered to only contain the columns with
match states to the HMM, which has a one to one mapping to the
query sequence.
Paramters
---------
alignment_result : dict
Alignment result dictionary, output by run_hmmsearch
prefix : str
Prefix for file creation
Returns
-------
str
path to raw focus alignment file
"""
def _add_gaps_to_query(query_sequence_ali, ali):
# get the index of columns that do not contain match states (indicated by an x)
gap_index = [
i for i, x in enumerate(ali.annotation["GC"]["RF"]) if x != "x"
]
# get the index of columns that contain match states (indicated by an x)
match_index = [
i for i, x in enumerate(ali.annotation["GC"]["RF"]) if x == "x"
]
# ensure that the length of the match states
# match the length of the sequence
if len(match_index) != query_sequence_ali.L:
raise ValueError("HMMsearch result {} does not have a one-to-one"
" mapping to the query sequence columns".format(
ar["raw_alignment_file"]))
gapped_query_sequence = ""
seq = list(query_sequence_ali.matrix[0, :])
# loop through every position in the HMMsearch hits
for i in range(len(ali.annotation["GC"]["RF"])):
# if that position should be a gap, add a gap
if i in gap_index:
gapped_query_sequence += "-"
# if that position should be a letter, pop the next
# letter in the query sequence
else:
gapped_query_sequence += seq.pop(0)
new_sequence_ali = Alignment.from_dict(
{query_sequence_ali.ids[0]: gapped_query_sequence})
return new_sequence_ali
# open the sequence file
with open(alignment_result["target_sequence_file"]) as a:
query_sequence_ali = Alignment.from_file(a, format="fasta")
# if the provided alignment is empty, just return the target sequence
raw_focus_alignment_file = prefix + "_raw.fasta"
if not valid_file(alignment_result["raw_alignment_file"]):
# write the query sequence to a fasta file
with open(raw_focus_alignment_file, "w") as of:
query_sequence_ali.write(of)
# return as an alignment object
return raw_focus_alignment_file
# else, open the HMM search result
with open(alignment_result["raw_alignment_file"]) as a:
ali = Alignment.from_file(a, format="stockholm")
# make sure that the stockholm alignment contains the match annotation
if not ("GC" in ali.annotation and "RF" in ali.annotation["GC"]):
raise ValueError("Stockholm alignment {} missing RF"
" annotation of match states".format(
alignment_result["raw_alignment_file"]))
# add insertions to the query sequence in order to preserve correct
# numbering of match sequences
gapped_sequence_ali = _add_gaps_to_query(query_sequence_ali, ali)
# write a new alignment file with the query sequence as
# the first entry
with open(raw_focus_alignment_file, "w") as of:
gapped_sequence_ali.write(of)
ali.write(of)
return raw_focus_alignment_file
def existing(**kwargs):
"""
Protocol:
Use external sequence alignment and extract all relevant
information from there (e.g. sequence, region, etc.),
then apply gap & fragment filtering as usual
Parameters
----------
Mandatory kwargs arguments:
See list below in code where calling check_required
Returns
-------
outcfg : dict
Output configuration of the pipeline, including
the following fields:
* sequence_id (passed through from input)
* alignment_file
* raw_focus_alignment_file
* statistics_file
* sequence_file
* first_index
* target_sequence_file
* annotation_file (None)
* frequencies_file
* identities_file
* focus_mode
* focus_sequence
* segments
"""
check_required(kwargs, [
"prefix", "input_alignment", "sequence_id", "first_index",
"extract_annotation"
])
prefix = kwargs["prefix"]
# make sure output directory exists
create_prefix_folders(prefix)
# this file is starting point of pipeline;
# check if input alignment actually exists
input_alignment = kwargs["input_alignment"]
verify_resources("Input alignment does not exist", input_alignment)
# first try to autodetect format of alignment
with open(input_alignment) as f:
format = detect_format(f)
if format is None:
raise InvalidParameterError(
"Format of input alignment {} could not be "
"automatically detected.".format(input_alignment))
with open(input_alignment) as f:
ali_raw = Alignment.from_file(f, format)
# save annotation in sequence headers (species etc.)
annotation_file = None
if kwargs["extract_annotation"]:
annotation_file = prefix + "_annotation.csv"
from_anno_line = (format == "stockholm")
annotation = extract_header_annotation(ali_raw,
from_annotation=from_anno_line)
annotation.to_csv(annotation_file, index=False)
# Target sequence of alignment
sequence_id = kwargs["sequence_id"]
if sequence_id is None:
raise InvalidParameterError("Parameter sequence_id must be defined")
# First, find focus sequence in alignment
focus_index = None
for i, id_ in enumerate(ali_raw.ids):
if id_.startswith(sequence_id):
focus_index = i
break
# if we didn't find it, cannot continue
if focus_index is None:
raise InvalidParameterError(
"Target sequence {} could not be found in alignment".format(
sequence_id))
# identify what columns (non-gap) to keep for focus
focus_seq = ali_raw[focus_index]
focus_cols = np.array([
c not in [ali_raw._match_gap, ali_raw._insert_gap] for c in focus_seq
])
# extract focus alignment
focus_ali = ali_raw.select(columns=focus_cols)
focus_seq_nogap = "".join(focus_ali[focus_index])
# determine region of sequence. If first_index is given,
# use that in any case, otherwise try to autodetect
full_focus_header = ali_raw.ids[focus_index]
focus_id = full_focus_header.split()[0]
# try to extract region from sequence header
id_, region_start, region_end = parse_header(focus_id)
# override with first_index if given
if kwargs["first_index"] is not None:
region_start = kwargs["first_index"]
region_end = region_start + len(focus_seq_nogap) - 1
if region_start is None or region_end is None:
raise InvalidParameterError(
"Could not extract region information " +
"from sequence header {} ".format(full_focus_header) +
"and first_index parameter is not given.")
# resubstitute full sequence ID from identifier
# and region information
header = "{}/{}-{}".format(id_, region_start, region_end)
focus_ali.ids[focus_index] = header
# write target sequence to file
target_sequence_file = prefix + ".fa"
with open(target_sequence_file, "w") as f:
write_fasta([(header, focus_seq_nogap)], f)
# apply sequence identity and fragment filters,
# and gap threshold
mod_outcfg, ali = modify_alignment(focus_ali, focus_index, id_,
region_start, **kwargs)
# generate output configuration of protocol
outcfg = {
**mod_outcfg,
"sequence_id": sequence_id,
"sequence_file": target_sequence_file,
"first_index": region_start,
"target_sequence_file": target_sequence_file,
"focus_sequence": header,
"focus_mode": True,
}
if annotation_file is not None:
outcfg["annotation_file"] = annotation_file
# dump config to YAML file for debugging/logging
write_config_file(prefix + ".align_existing.outcfg", outcfg)
# return results of protocol
return outcfg
def _format_alignment_for_hmmbuild(input_alignment_file, **kwargs):
# this file is starting point of pipeline;
# check if input alignment actually exists
verify_resources("Input alignment does not exist",
input_alignment_file)
# first try to autodetect format of alignment
with open(input_alignment_file) as f:
format = detect_format(f)
if format is None:
raise InvalidParameterError(
"Format of input alignment {} could not be "
"automatically detected.".format(input_alignment_file))
with open(input_alignment_file) as f:
ali_raw = Alignment.from_file(f, format)
# Target sequence of alignment
sequence_id = kwargs["sequence_id"]
if sequence_id is None:
raise InvalidParameterError(
"Parameter sequence_id must be defined")
# First, find focus sequence in alignment
focus_index = None
for i, id_ in enumerate(ali_raw.ids):
if id_.startswith(sequence_id):
focus_index = i
break
# if we didn't find it, cannot continue
if focus_index is None:
raise InvalidParameterError(
"Target sequence {} could not be found in alignment".format(
sequence_id))
# identify what columns (non-gap) to keep for focus
# this should be all columns in the raw_focus_alignment_file
# but checking anyway
focus_seq = ali_raw[focus_index]
focus_cols = np.array([
c not in [ali_raw._match_gap, ali_raw._insert_gap]
for c in focus_seq
])
# extract focus alignment
focus_ali = ali_raw.select(columns=focus_cols)
focus_seq_nogap = "".join(focus_ali[focus_index])
# determine region of sequence. If first_index is given,
# use that in any case, otherwise try to autodetect
full_focus_header = ali_raw.ids[focus_index]
focus_id = full_focus_header.split()[0]
# try to extract region from sequence header
id_, region_start, region_end = parse_header(focus_id)
# override with first_index if given
if kwargs["first_index"] is not None:
region_start = kwargs["first_index"]
region_end = region_start + len(focus_seq_nogap) - 1
if region_start is None or region_end is None:
raise InvalidParameterError(
"Could not extract region information " +
"from sequence header {} ".format(full_focus_header) +
"and first_index parameter is not given.")
# resubstitute full sequence ID from identifier
# and region information
header = "{}/{}-{}".format(id_, region_start, region_end)
focus_ali.ids[focus_index] = header
# write target sequence to file
target_sequence_file = prefix + ".fa"
with open(target_sequence_file, "w") as f:
write_fasta([(header, focus_seq_nogap)], f)
# swap target sequence to first position if it is not
# the first sequence in alignment;
# this is particularly important for hhfilter run
# because target sequence might otherwise be filtered out
if focus_index != 0:
indices = np.arange(0, len(focus_ali))
indices[0] = focus_index
indices[focus_index] = 0
focus_index = 0
focus_ali = focus_ali.select(sequences=indices)
# write the raw focus alignment for hmmbuild
focus_fasta_file = prefix + "_raw_focus_input.fasta"
with open(focus_fasta_file, "w") as f:
focus_ali.write(f, "fasta")
return focus_fasta_file, target_sequence_file, region_start, region_end
def standard(**kwargs):
"""
Protocol:
Standard buildali4 workflow (run iterative jackhmmer
search against sequence database, than determine which
sequences and columns to include in the calculation based
on coverage and maximum gap thresholds).
Parameters
----------
Mandatory kwargs arguments:
See list below in code where calling check_required
Returns
-------
outcfg : dict
Output configuration of the pipeline, including
the following fields:
* sequence_id (passed through from input)
* first_index (passed through from input)
* alignment_file
* raw_alignment_file
* raw_focus_alignment_file
* statistics_file
* target_sequence_file
* sequence_file
* annotation_file
* frequencies_file
* identities_file
* hittable_file
* focus_mode
* focus_sequence
* segments
ali : Alignment
Final sequence alignment
"""
check_required(kwargs, [
"prefix",
"extract_annotation",
])
prefix = kwargs["prefix"]
# make sure output directory exists
create_prefix_folders(prefix)
# first step of protocol is to get alignment using
# jackhmmer; initialize output configuration with
# results of this search
jackhmmer_outcfg = jackhmmer_search(**kwargs)
stockholm_file = jackhmmer_outcfg["raw_alignment_file"]
segment = Segment.from_list(jackhmmer_outcfg["segments"][0])
target_seq_id = segment.sequence_id
region_start = segment.region_start
region_end = segment.region_end
# read in stockholm format (with full annotation)
with open(stockholm_file) as a:
ali_raw = Alignment.from_file(a, "stockholm")
# and store as FASTA file first (disabled for now
# since equivalent information easily be obtained
# from Stockholm file
"""
ali_raw_fasta_file = prefix + "_raw.fasta"
with open(ali_raw_fasta_file, "w") as f:
ali_raw.write(f, "fasta")
"""
# save annotation in sequence headers (species etc.)
if kwargs["extract_annotation"]:
annotation_file = prefix + "_annotation.csv"
annotation = extract_header_annotation(ali_raw)
annotation.to_csv(annotation_file, index=False)
# center alignment around focus/search sequence
focus_cols = np.array([c != "-" for c in ali_raw[0]])
focus_ali = ali_raw.select(columns=focus_cols)
target_seq_index = 0
mod_outcfg, ali = modify_alignment(focus_ali, target_seq_index,
target_seq_id, region_start, **kwargs)
# merge results of jackhmmer_search and modify_alignment stage
outcfg = {
**jackhmmer_outcfg,
**mod_outcfg, "annotation_file": annotation_file
}
# dump output config to YAML file for debugging/logging
write_config_file(prefix + ".align_standard.outcfg", outcfg)
# return results of protocol
return outcfg
def find_homologs(pdb_alignment_method="jackhmmer", **kwargs):
"""
Identify homologs using jackhmmer or hmmbuild/hmmsearch
Parameters
----------
pdb_alignment_method : {"jackhmmer", "hmmsearch"},
optional (default: "jackhmmer")
Sequence alignment method used for searching the PDB
**kwargs
Passed into jackhmmer / hmmbuild_and_search protocol
(see documentation for available options)
Returns
-------
ali : evcouplings.align.Alignment
Alignment of homologs of query sequence
in sequence database
hits : pandas.DataFrame
Tabular representation of hits
"""
# load default configuration
config = parse_config(HMMER_CONFIG)
# update with overrides from kwargs
config = {
**config,
**kwargs,
}
# create temporary output if no prefix is given
if config["prefix"] is None:
config["prefix"] = path.join(tempdir(), "compare")
check_required(config, ["prefix"])
# run hmmsearch (possibly preceded by hmmbuild)
if pdb_alignment_method == "hmmsearch":
# set up config to run hmmbuild_and_search on the unfiltered alignment file
updated_config = deepcopy(config)
updated_config["alignment_file"] = config.get(
"raw_focus_alignment_file")
ar = hmmbuild_and_search(**updated_config)
# For hmmbuild and search, we have to read the raw focus alignment file
# to guarantee that the query sequence is present
with open(ar["raw_focus_alignment_file"]) as a:
ali = Alignment.from_file(a, "fasta")
# run jackhmmer against sequence database
# at this point we have already checked to ensure
# that the input is either jackhmmer or hmmsearch
elif pdb_alignment_method == "jackhmmer":
ar = jackhmmer_search(**config)
with open(ar["raw_alignment_file"]) as a:
ali = Alignment.from_file(a, "stockholm")
# write alignment as FASTA file for easier checking by hand,
# if necessary
with open(config["prefix"] + "_raw.fasta", "w") as f:
ali.write(f)
else:
raise InvalidParameterError(
"Invalid pdb_alignment_method selected. Valid options are: " +
", ".join(["jackhmmer", "hmmsearch"]))
# read hmmer hittable and simplify
hits = read_hmmer_domtbl(ar["hittable_file"])
hits.loc[:, "uniprot_ac"] = hits.loc[:, "target_name"].map(
lambda x: x.split("|")[1])
hits.loc[:, "uniprot_id"] = hits.loc[:, "target_name"].map(
lambda x: x.split("|")[2])
hits = hits.rename(
columns={
"domain_score": "bitscore",
"domain_i_Evalue": "e_value",
"ali_from": "alignment_start",
"ali_to": "alignment_end",
"hmm_from": "hmm_start",
"hmm_to": "hmm_end",
})
hits.loc[:, "alignment_start"] = pd.to_numeric(
hits.alignment_start).astype(int)
hits.loc[:,
"alignment_end"] = pd.to_numeric(hits.alignment_end).astype(int)
hits.loc[:, "alignment_id"] = (hits.target_name + "/" +
hits.alignment_start.astype(str) + "-" +
hits.alignment_end.astype(str))
hits = hits.loc[:, [
"alignment_id", "uniprot_ac", "uniprot_id", "alignment_start",
"alignment_end", "bitscore", "e_value"
]]
return ali, hits
def mean_field(**kwargs):
"""
Protocol:
Infer ECs from alignment using mean field direct coupling analysis.
For now, mean field DCA can only be run in focus mode, gaps
included.
Parameters
----------
Mandatory kwargs arguments:
See list below in code where calling check_required.
Returns
-------
outcfg : dict
Output configuration of the pipeline, including
the following fields:
* raw_ec_file
* model_file
* num_sites
* num_sequences
* effective_sequences
* focus_mode (passed through)
* focus_sequence (passed through)
* segments (passed through)
"""
check_required(
kwargs,
[
"prefix", "alignment_file", "segments",
"focus_mode", "focus_sequence", "theta",
"pseudo_count", "alphabet",
"min_sequence_distance", # "save_model",
]
)
if not kwargs["focus_mode"]:
raise InvalidParameterError(
"For now, mean field DCA can only be run in focus mode."
)
prefix = kwargs["prefix"]
# option to save model disabled
"""
if kwargs["save_model"]:
model = prefix + ".model"
else:
model = None
"""
model = prefix + ".model"
outcfg = {
"model_file": model,
"raw_ec_file": prefix + "_ECs.txt",
"ec_file": prefix + "_CouplingScores.csv",
# TODO: the following are passed through stage...
# keep this or unnecessary?
"focus_mode": kwargs["focus_mode"],
"focus_sequence": kwargs["focus_sequence"],
"segments": kwargs["segments"],
}
# make sure input alignment exists
alignment_file = kwargs["alignment_file"]
verify_resources(
"Input alignment does not exist",
kwargs["alignment_file"]
)
# make sure output directory exists
create_prefix_folders(prefix)
segments = kwargs["segments"]
if segments is not None:
segments = [
mapping.Segment.from_list(s) for s in segments
]
# determine alphabet
# default is protein
if kwargs["alphabet"] is None:
alphabet = ALPHABET_PROTEIN
else:
alphabet = kwargs["alphabet"]
# allow shortcuts for protein, DNA, RNA
if alphabet in ALPHABET_MAP:
alphabet = ALPHABET_MAP[alphabet]
# read in a2m alignment
with open(alignment_file) as f:
input_alignment = Alignment.from_file(
f, alphabet=alphabet,
format="fasta"
)
# init mean field direct coupling analysis
mf_dca = MeanFieldDCA(input_alignment)
# run mean field approximation
model = mf_dca.fit(
theta=kwargs["theta"],
pseudo_count=kwargs["pseudo_count"]
)
# write ECs to file
model.to_raw_ec_file(
outcfg["raw_ec_file"]
)
# write model file
if outcfg["model_file"] is not None:
model.to_file(
outcfg["model_file"],
file_format="plmc_v2"
)
# store useful information about model in outcfg
outcfg.update({
"num_sites": model.L,
"num_valid_sequences": model.N_valid,
"effective_sequences": float(round(model.N_eff, 1)),
"region_start": int(model.index_list[0]),
})
# read and sort ECs
ecs = pd.read_csv(
outcfg["raw_ec_file"], sep=" ",
# for now, call the last two columns
# "fn" and "cn" to prevent compare
# stage from crashing
names=["i", "A_i", "j", "A_j", "fn", "cn"]
# names=["i", "A_i", "j", "A_j", "mi", "di"]
).sort_values(
by="cn",
ascending=False
)
is_single_segment = segments is None or len(segments) == 1
outcfg = {
**outcfg,
**_postprocess_inference(
ecs, kwargs, model, outcfg, prefix,
generate_enrichment=is_single_segment,
generate_line_plot=is_single_segment
)
}
# dump output config to YAML file for debugging/logging
write_config_file(prefix + ".couplings_meanfield.outcfg", outcfg)
return outcfg
def find_homologs_jackhmmer(**kwargs):
"""
Identify homologs using jackhmmer
Parameters
----------
**kwargs
Passed into jackhmmer_search protocol
(see documentation for available options)
Returns
-------
ali : evcouplings.align.Alignment
Alignment of homologs of query sequence
in sequence database
hits : pandas.DataFrame
Tabular representation of hits
"""
# load default configuration
config = parse_config(JACKHMMER_CONFIG)
# update with overrides from kwargs
config = {
**config,
**kwargs,
}
# create temporary output if no prefix is given
if config["prefix"] is None:
config["prefix"] = path.join(tempdir(), "compare")
# run jackhmmer against sequence database
ar = jackhmmer_search(**config)
with open(ar["raw_alignment_file"]) as a:
ali = Alignment.from_file(a, "stockholm")
# write alignment as FASTA file for easier checking by hand,
# if necessary
with open(config["prefix"] + "_raw.fasta", "w") as f:
ali.write(f)
# read hmmer hittable and simplify
hits = read_hmmer_domtbl(ar["hittable_file"])
hits.loc[:, "uniprot_ac"] = hits.loc[:, "target_name"].map(
lambda x: x.split("|")[1])
hits.loc[:, "uniprot_id"] = hits.loc[:, "target_name"].map(
lambda x: x.split("|")[2])
hits = hits.rename(
columns={
"domain_score": "bitscore",
"domain_i_Evalue": "e_value",
"ali_from": "alignment_start",
"ali_to": "alignment_end",
})
hits.loc[:, "alignment_start"] = pd.to_numeric(
hits.alignment_start).astype(int)
hits.loc[:,
"alignment_end"] = pd.to_numeric(hits.alignment_end).astype(int)
hits.loc[:, "alignment_id"] = (hits.target_name + "/" +
hits.alignment_start.astype(str) + "-" +
hits.alignment_end.astype(str))
hits = hits.loc[:, [
"alignment_id", "uniprot_ac", "uniprot_id", "alignment_start",
"alignment_end", "bitscore", "e_value"
]]
return ali, hits
def mean_field(**kwargs):
"""
Protocol:
Infer ECs from alignment using mean field direct coupling analysis.
For now, mean field DCA can only be run in focus mode, gaps
included.
Parameters
----------
Mandatory kwargs arguments:
See list below in code where calling check_required.
Returns
-------
outcfg : dict
Output configuration of the pipeline, including
the following fields:
* raw_ec_file
* model_file
* num_sites
* num_sequences
* effective_sequences
* focus_mode (passed through)
* focus_sequence (passed through)
* segments (passed through)
"""
check_required(
kwargs,
[
"prefix", "alignment_file", "segments",
"focus_mode", "focus_sequence", "theta",
"pseudo_count", "alphabet",
"min_sequence_distance", # "save_model",
]
)
if not kwargs["focus_mode"]:
raise InvalidParameterError(
"For now, mean field DCA can only be run in focus mode."
)
prefix = kwargs["prefix"]
# option to save model disabled
"""
if kwargs["save_model"]:
model = prefix + ".model"
else:
model = None
"""
model = prefix + ".model"
outcfg = {
"model_file": model,
"raw_ec_file": prefix + "_ECs.txt",
"ec_file": prefix + "_CouplingScores.csv",
# TODO: the following are passed through stage...
# keep this or unnecessary?
"focus_mode": kwargs["focus_mode"],
"focus_sequence": kwargs["focus_sequence"],
"segments": kwargs["segments"],
}
# make sure input alignment exists
alignment_file = kwargs["alignment_file"]
verify_resources(
"Input alignment does not exist",
kwargs["alignment_file"]
)
# make sure output directory exists
create_prefix_folders(prefix)
segments = kwargs["segments"]
if segments is not None:
segments = [
mapping.Segment.from_list(s) for s in segments
]
# determine alphabet
# default is protein
if kwargs["alphabet"] is None:
alphabet = ALPHABET_PROTEIN
else:
alphabet = kwargs["alphabet"]
# allow shortcuts for protein, DNA, RNA
if alphabet in ALPHABET_MAP:
alphabet = ALPHABET_MAP[alphabet]
# read in a2m alignment
with open(alignment_file) as f:
input_alignment = Alignment.from_file(
f, alphabet=alphabet,
format="fasta"
)
# init mean field direct coupling analysis
mf_dca = MeanFieldDCA(input_alignment)
# run mean field approximation
model = mf_dca.fit(
theta=kwargs["theta"],
pseudo_count=kwargs["pseudo_count"]
)
# write ECs to file
model.to_raw_ec_file(
outcfg["raw_ec_file"]
)
# write model file
if outcfg["model_file"] is not None:
model.to_file(
outcfg["model_file"],
file_format="plmc_v2"
)
# store useful information about model in outcfg
outcfg.update({
"num_sites": model.L,
"num_sequences": model.N_valid,
"effective_sequences": float(round(model.N_eff, 1)),
"region_start": int(model.index_list[0]),
})
# read and sort ECs
ecs = pd.read_csv(
outcfg["raw_ec_file"], sep=" ",
# for now, call the last two columns
# "fn" and "cn" to prevent compare
# stage from crashing
names=["i", "A_i", "j", "A_j", "fn", "cn"]
# names=["i", "A_i", "j", "A_j", "mi", "di"]
).sort_values(
by="cn",
ascending=False
)
# write the sorted ECs table to csv file
ecs.to_csv(outcfg["ec_file"], index=False)
# also store longrange ECs as convenience output
if kwargs["min_sequence_distance"] is not None:
outcfg["ec_longrange_file"] = prefix + "_CouplingScores_longrange.csv"
ecs_longrange = ecs.query(
"abs(i - j) >= {}".format(kwargs["min_sequence_distance"])
)
ecs_longrange.to_csv(outcfg["ec_longrange_file"], index=False)
# also create line-drawing script (for now, only for single segments)
if segments is None or len(segments) == 1:
outcfg["ec_lines_pml_file"] = prefix + "_draw_ec_lines.pml"
L = outcfg["num_sites"]
ec_lines_pymol_script(
ecs_longrange.iloc[:L, :],
outcfg["ec_lines_pml_file"],
score_column="cn" # "di
)
# compute EC enrichment (for now, for single segments
# only since enrichment code cannot handle multiple segments)
if segments is None or len(segments) == 1:
outcfg["enrichment_file"] = prefix + "_enrichment.csv"
ecs_enriched = pairs.enrichment(ecs, score="cn") # "di"
ecs_enriched.to_csv(outcfg["enrichment_file"], index=False)
# create corresponding enrichment pymol scripts
outcfg["enrichment_pml_files"] = []
for sphere_view, pml_suffix in [
(True, "_enrichment_spheres.pml"), (False, "_enrichment_sausage.pml")
]:
pml_file = prefix + pml_suffix
enrichment_pymol_script(ecs_enriched, pml_file, sphere_view=sphere_view)
outcfg["enrichment_pml_files"].append(pml_file)
# output EVzoom JSON file if we have stored model file
if outcfg.get("model_file", None) is not None:
outcfg["evzoom_file"] = prefix + "_evzoom.json"
with open(outcfg["evzoom_file"], "w") as f:
# create JSON output and write to file
f.write(
evzoom_json(model) + "\n"
)
# dump output config to YAML file for debugging/logging
write_config_file(prefix + ".couplings_standard.outcfg", outcfg)
return outcfg
def filter_best_reciprocal(alignment,
paralogs,
most_similar_in_species,
allowed_error=0.02):
"""
Takes in a dictionary of the best hit to each genome
Removes sequences that are not the best reciprocal hit to the query sequence
Parameters
----------
alignment : str
Path to sequence alignment file
paralogs : pd.DataFrame
Rows correspond to paralogs to the query sequence
Created by find_paralogs() function
most_similar_in_species : pd.DataFrame
Contains the id, species name, and percent identity to query
for each sequence that was the best hit to the query in its
respective species
allowed_error : float
In order for a sequence to be filtered out of the alignment,
it must be more identitical to a paralog sequence than the
target sequence by at least this amount
Returns
-------
pd.DataFrame
Contains the id, species name, and percenty identity to query
for each sequence that was the best reciprocal hit to the query sequence
"""
with open(alignment, "r") as inf:
ali = Alignment.from_file(inf)
# Create an n_paralogs x n_sequences ndarray
# where entry i,j is percent identity of paralog i to sequence j
# note the identity here will be different than for the unfiltered alignment
# initialize the matrix
identity_mat = np.zeros((len(paralogs), len(ali.ids)), dtype=float)
for idx, paralog_id in enumerate(paralogs.id):
# calculate the % identity of every seq in the alignment to current paralog
identities = ali.identities_to(ali[ali.id_to_index[paralog_id]])
# save the results
identity_mat[idx, :] = identities
indices_to_keep = []
# for every sequence in the alignment that is the most similar to the query
# in its respective species...
for index, row in most_similar_in_species.iterrows():
# get the index of that sequence in the alignment.
alignment_index = ali.id_to_index[row.id]
# Keep sequences if they are the best reciprocal hit -
# i.e., that sequence is not more similar to any paralog
# than it is to the query sequence
if np.all(identity_mat[:, alignment_index] < row.identity_to_query +
allowed_error):
indices_to_keep.append(index)
return most_similar_in_species.loc[indices_to_keep, :]
def alignment_index_mapping(alignment_file,
format="stockholm",
target_seq=None):
"""
Create index mapping table between sequence positions
based on a sequence alignment.
Parameters
----------
alignment_file : str
Path of alignment file containing sequences for
which indices shoul dbe mapped
format : {"stockholm", "fasta"}
Format of alignment file
target_seq : str, optional (default: None)
Identifier of sequence around which the index
mapping will be centered. If None, first sequence
in alignment will be used.
Returns
-------
pandas.DataFrame
Mapping table containing assignment of
1. index in target sequence (i)
2. symbol in target sequence (A_i)
For all other sequences in alignment, the following
two columns:
3. index in second sequence (j_<sequence id>)
4. symbol in second sequence (A_j_<sequence_id>)
"""
# read alignment that is basis of mapping
with open(alignment_file) as a:
ali = Alignment.from_file(a, format)
# determine index of target sequence if necessary
# (default: first sequence in alignment)
if target_seq is None:
target_seq_index = 0
else:
for i, full_id in enumerate(ali.ids):
if full_id.startswith(target_seq):
target_seq_index = i
# get range and sequence of target
id_, target_start, target_end = parse_header(ali.ids[target_seq_index])
target_seq = ali.matrix[target_seq_index]
# now map from target numbering to hit numbering
full_map = None
for i, full_id in enumerate(ali.ids):
if i == target_seq_index:
continue
# extract information about sequence we are comparing to
id_, region_start, region_end = parse_header(full_id)
other_seq = ali.matrix[i]
# compute mapping table
map_df = map_indices(target_seq, target_start, target_end, other_seq,
region_start, region_end,
[ali._match_gap, ali._insert_gap])
# adjust column names for non-target sequence
map_df = map_df.rename(columns={
"j": "i_" + full_id,
"A_j": "A_i_" + full_id,
})
# add to full mapping table, left outer join
# so all positions in target sequence are kept
if full_map is None:
full_map = map_df
else:
full_map = full_map.merge(map_df, on=("i", "A_i"), how="left")
return full_map
def mean_field(**kwargs):
"""
Protocol:
Infer ECs from alignment using mean field direct coupling analysis.
For now, mean field DCA can only be run in focus mode, gaps
included.
Parameters
----------
Mandatory kwargs arguments:
See list below in code where calling check_required.
Returns
-------
outcfg : dict
Output configuration of the pipeline, including
the following fields:
* raw_ec_file
* model_file
* num_sites
* num_sequences
* effective_sequences
* focus_mode (passed through)
* focus_sequence (passed through)
* segments (passed through)
"""
check_required(
kwargs,
[
"prefix", "alignment_file", "segments",
"focus_mode", "focus_sequence", "theta",
"pseudo_count", "alphabet",
"min_sequence_distance", # "save_model",
"ec_score_type",
]
)
if not kwargs["focus_mode"]:
raise InvalidParameterError(
"For now, mean field DCA can only be run in focus mode."
)
prefix = kwargs["prefix"]
# option to save model disabled
"""
if kwargs["save_model"]:
model = prefix + ".model"
else:
model = None
"""
model = prefix + ".model"
outcfg = {
"model_file": model,
"raw_ec_file": prefix + "_ECs.txt",
"ec_file": prefix + "_CouplingScores.csv",
# TODO: the following are passed through stage...
# keep this or unnecessary?
"focus_mode": kwargs["focus_mode"],
"focus_sequence": kwargs["focus_sequence"],
"segments": kwargs["segments"],
}
# make sure input alignment exists
alignment_file = kwargs["alignment_file"]
verify_resources(
"Input alignment does not exist",
kwargs["alignment_file"]
)
# make sure output directory exists
create_prefix_folders(prefix)
segments = kwargs["segments"]
if segments is not None:
segments = [
mapping.Segment.from_list(s) for s in segments
]
# determine alphabet
# default is protein
if kwargs["alphabet"] is None:
alphabet = ALPHABET_PROTEIN
else:
alphabet = kwargs["alphabet"]
# allow shortcuts for protein, DNA, RNA
if alphabet in ALPHABET_MAP:
alphabet = ALPHABET_MAP[alphabet]
# read in a2m alignment
with open(alignment_file) as f:
input_alignment = Alignment.from_file(
f, alphabet=alphabet,
format="fasta"
)
# init mean field direct coupling analysis
mf_dca = MeanFieldDCA(input_alignment)
# run mean field approximation
model = mf_dca.fit(
theta=kwargs["theta"],
pseudo_count=kwargs["pseudo_count"]
)
# write ECs to file
model.to_raw_ec_file(
outcfg["raw_ec_file"]
)
# write model file
if outcfg["model_file"] is not None:
model.to_file(
outcfg["model_file"],
file_format="plmc_v2"
)
# store useful information about model in outcfg
outcfg.update({
"num_sites": model.L,
"num_valid_sequences": model.N_valid,
"effective_sequences": float(round(model.N_eff, 1)),
"region_start": int(model.index_list[0]),
})
# read and sort ECs
# Note: this now deviates from the original EC format
# file because it has 4 score columns to accomodate
# MI (raw), MI (APC-corrected), DI, CN;
ecs = pd.read_csv(
outcfg["raw_ec_file"], sep=" ",
names=["i", "A_i", "j", "A_j", "mi_raw", "mi_apc", "di", "cn"]
)
# select target score;
# by default select CN score, since it allows to compute probabilities etc.
ec_score_type = kwargs.get("ec_score_type", "cn")
valid_ec_type_choices = ["cn", "di", "mi_raw", "mi_apc"]
if ec_score_type not in valid_ec_type_choices:
raise InvalidParameterError(
"Invalid choice for valid_ec_type: {}, valid options are: {}".format(
ec_score_type, ", ".join(valid_ec_type_choices)
)
)
# perform rescoring if CN score is selected, otherwise cannot rescore
# since all models are based on distribution shapes generated by CN score
if ec_score_type == "cn":
# perform EC rescoring starting from CN score output by plmc;
# outconfig update will be merged further down in final outcfg merge
# returned list is already sorted
ecs, rescorer_outcfg_update = rescore_cn_score_ecs(
ecs, segments, outcfg, kwargs, score="cn"
)
else:
# If MI or DI, cannot apply distribution-based rescoring approaches,
# so just set score column and add dummy probability value for compatibility
# with downstream code
ecs = ecs.assign(
score=ecs[ec_score_type],
probability=np.nan
).sort_values(
by="score",
ascending=False
)
# no additional values to be updated in outcfg in this case
rescorer_outcfg_update = {}
is_single_segment = segments is None or len(segments) == 1
outcfg = {
**outcfg,
**rescorer_outcfg_update,
**_postprocess_inference(
ecs, kwargs, model, outcfg, prefix,
generate_enrichment=is_single_segment,
generate_line_plot=is_single_segment,
score="score"
)
}
# dump output config to YAML file for debugging/logging
write_config_file(prefix + ".couplings_meanfield.outcfg", outcfg)
return outcfg