class Peptides(object):
"""
::
>>> p = Peptides()
>>> p.get_fasta_sequence("Q8IYB3")
>>> p.get_peptide_position("Q8IYB3", "VPKPEPIPEPKEPSPE")
189
Sometimes, peptides are provided with a pattern indicating the phospho site.
e.g., ::
>>>
"""
def __init__(self, verbose=False):
self.u = UniProt(verbose=verbose)
self.sequences = {}
def get_fasta_sequence(self, uniprot_name):
seq = self.u.get_fasta_sequence(uniprot_name)
return seq
def get_phosphosite_position(self, uniprot_name, peptide):
if uniprot_name not in self.sequences.keys():
seq = self.get_fasta_sequence(uniprot_name)
self.sequences[uniprot_name] = seq[:]
else:
seq = self.sequences[uniprot_name][:]
positions = [x.start() for x in re.finditer("PQS", seq)]
return positions
def add_sequence_to_nodes(n: str, d: Dict[str, Any]):
"""
Maps UniProt ACC to UniProt ID. Retrieves sequence from UniProt and adds it to the node as a feature
:param n: Graph node.
:type n: str
:param d: Graph attribute dictionary.
:type d: Dict[str, Any]
"""
h = HGNC(verbose=False)
u = UniProt(verbose=False)
d["uniprot_ids"] = h.fetch(
"symbol", d["protein_id"])["response"]["docs"][0]["uniprot_ids"]
# Todo these API calls should probably be batched
# Todo mapping with bioservices to support other protein IDs?
for id in d["uniprot_ids"]:
d[f"sequence_{id}"] = u.get_fasta_sequence(id)
def make_files(out_dir=os.path.dirname(os.path.realpath(__file__))):
# Initialize
cwd = os.getcwd()
matrix_ids = set()
codec = coreapi.codecs.CoreJSONCodec()
uniprot = UniProt(verbose=False, cache=False)
# Create output dir
if not os.path.exists(out_dir):
os.makedirs(out_dir)
# For each taxon...
for taxon in taxons:
# Skip if taxon profiles JSON file already exists
profiles_json_file = os.path.join(
out_dir, "%s.profiles.json" % taxon)
if not os.path.exists(profiles_json_file):
try:
# Initialize
profiles = {}
client = coreapi.Client()
response = client.get(
"http://jaspar.genereg.net/api/v1/taxon/%s/" % taxon)
json_obj = json.loads(codec.encode(response))
# While there are more pages...
while json_obj["next"] is not None:
# For each profile...
for profile in json_obj["results"]:
# If CORE collection profile...
if profile["collection"] == "CORE":
# Add profile
profiles.setdefault(profile["matrix_id"], profile["name"])
# Go to next page
response = client.get(json_obj["next"])
json_obj = json.loads(codec.encode(response))
# Do last page
for profile in json_obj["results"]:
# If CORE collection profile...
if profile["collection"] == "CORE":
# Add profile
profiles.setdefault(profile["matrix_id"], profile["name"])
# Write
functions.write(profiles_json_file, json.dumps(
profiles, sort_keys=True, indent=4, separators=(",", ": ")))
except:
raise ValueError("Could not fetch %s profiles from JASPAR" % taxon)
# Skip if taxon uniprot JSON file already exists
uniprot_json_file = os.path.join(out_dir, "%s.uniprot.json" % taxon)
if not os.path.exists(uniprot_json_file):
try:
# Initialize
uniaccs = {}
client = coreapi.Client()
# Load JSON file
with open(profiles_json_file) as f:
profiles = json.load(f)
# For each profile...
for profile in sorted(profiles):
# Get profile detailed info
response = client.get(
"http://jaspar.genereg.net/api/v1/matrix/%s/" % profile)
json_obj = json.loads(codec.encode(response))
# Fix bugged cases
if json_obj["matrix_id"] == "MA0328.1":
json_obj["uniprot_ids"] = ["P0CY08"]
if json_obj["matrix_id"] == "MA0110.1":
json_obj["uniprot_ids"] = ["P46667"]
if json_obj["matrix_id"] == "MA0058.1":
json_obj["uniprot_ids"] = ["P61244"]
if json_obj["matrix_id"] == "MA0046.1":
json_obj["uniprot_ids"] = ["P20823"]
if json_obj["matrix_id"] == "MA0098.1":
json_obj["uniprot_ids"] = ["P14921"]
if json_obj["matrix_id"] == "MA0052.1":
json_obj["uniprot_ids"] = ["Q02078"]
if json_obj["matrix_id"] == "MA0024.1":
json_obj["uniprot_ids"] = ["Q01094"]
if json_obj["matrix_id"] == "MA0138.1":
json_obj["uniprot_ids"] = ["Q13127"]
# For each UniProt Accession...
for uniacc in json_obj["uniprot_ids"]:
# Strip
uniacc = uniacc.strip(" ")
# Add uniacc
uniaccs.setdefault(uniacc, [[], None])
if profile not in uniaccs[uniacc][0]:
uniaccs[uniacc][0].append(profile)
# For each UniProt Accession...
for uniacc in uniaccs:
# Get UniProt sequence
uniaccs[uniacc][1] = uniprot.get_fasta_sequence(uniacc)
# Write
functions.write(uniprot_json_file, json.dumps(
uniaccs, sort_keys=True, indent=4, separators=(",", ": ")))
except:
raise ValueError("Could not fetch %s sequences from UniProt" % taxon)
# Skip if taxon FASTA file already exists
fasta_file = os.path.join(out_dir, "%s.fa" % taxon)
if not os.path.exists(fasta_file):
# Load JSON file
with open(uniprot_json_file) as f:
uniaccs = json.load(f)
# For each UniProt Accession...
for uniacc in sorted(uniaccs):
# Write
functions.write(fasta_file,
">%s\n%s" % (uniacc, uniaccs[uniacc][1]))
# Create BLAST+ db
try:
process = subprocess.check_output([
"makeblastdb",
"-in", fasta_file,
"-dbtype", "prot"],
stderr=subprocess.STDOUT)
except:
raise ValueError("Could not create BLAST+ database: %s" % fasta_file)
# Skip if Cis-BP JSON file already exists
cisbp_json_file = os.path.join(out_dir, "cisbp.json")
if not os.path.exists(cisbp_json_file):
# Initialize
proteins = {}
prot_features = {}
tfs = {}
tf_families = {}
# Create Cis-BP dir
cisbp_dir = os.path.join(out_dir, "cisbp")
if not os.path.exists(cisbp_dir):
os.makedirs(cisbp_dir)
# Change dir
os.chdir(cisbp_dir)
# Skip if TFs file already exists
if not os.path.exists("cisbp_1.02.tfs.sql"):
# Download SQL files
os.system("curl --silent -O http://cisbp.ccbr.utoronto.ca/data/1.02/DataFiles/SQLDumps/SQLArchive_cisbp_1.02.zip")
# Unzip
os.system("unzip -qq SQLArchive_cisbp_1.02.zip")
# Remove SQL files
os.remove("SQLArchive_cisbp_1.02.zip")
# For each ZIP file...
for zip_file in frozenset(os.listdir(os.getcwd())):
# Skip non-zip files
if not zip_file.endswith(".zip"): continue
# Unzip
os.system("unzip -qq %s" % zip_file)
os.remove(zip_file)
# Return to original dir
os.chdir(cwd)
# Get protein features
with open(os.path.join(cisbp_dir, "cisbp_1.02.prot_features.sql")) as f:
# For each line...
for line in f:
m = re.search("\('.+', '(.+)', '.+', \d+, \d+, '(.+)'\)", line)
if m:
prot_features.setdefault(m.group(1), set())
prot_features[m.group(1)].add(m.group(2))
# Get TFs
with open(os.path.join(cisbp_dir, "cisbp_1.02.tfs.sql")) as f:
# For each line...
for line in f:
m = re.search("\('(.+)', '(.+)', '.+', '.+', '.+', '.+', '.+'\)", line)
if m:
tfs.setdefault(m.group(1), m.group(2))
# Get TF families
with open(os.path.join(cisbp_dir, "cisbp_1.02.tf_families.sql")) as f:
# For each line...
for line in f:
m = re.search("\('(.+)', '.+', '.+', \d+, (.+)\)", line)
if m:
tf_families.setdefault(m.group(1), m.group(2))
# Get proteins
with open(os.path.join(cisbp_dir, "cisbp_1.02.proteins.sql")) as f:
# For each line...
for line in f:
m = re.search("\('(.+)', '(.+)', '.+', '.+', '([A-Z]+)\W*'\)", line)
if m:
if m.group(1) not in prot_features: continue
# Digest to MD5
h = hashlib.new("md5")
h.update(m.group(3).encode("utf-8"))
md5 = h.hexdigest() + m.group(3)[:4] + m.group(3)[-4:]
proteins.setdefault(md5, [tf_families[tfs[m.group(2)]], []])
# For each domain...
for domain in prot_features[m.group(1)]:
if domain not in proteins[md5][1]:
proteins[md5][1].append(domain)
# Write
functions.write(cisbp_json_file, json.dumps(
proteins, sort_keys=True, indent=4, separators=(",", ": ")))
# Remove Cis-BP dir
shutil.rmtree(cisbp_dir)
# Skip if JSON files already exist
domains_json_file = os.path.join(out_dir, "domains.json")
jaspar_json_file = os.path.join(out_dir, "jaspar.json")
if not os.path.exists(domains_json_file) or not os.path.exists(jaspar_json_file):
# Initialize
domains = {}
jaspar = {}
# Load JSON file
with open(cisbp_json_file) as f:
cisbp = json.load(f)
# Remove JSON files
if os.path.exists(domains_json_file): domains_json_file
if os.path.exists(jaspar_json_file): jaspar_json_file
# For each taxon...
for taxon in taxons:
# Load JSON files
profiles_json_file = os.path.join(
out_dir, "%s.profiles.json" % taxon)
with open(profiles_json_file) as f:
profiles = json.load(f)
uniprot_json_file = os.path.join(
out_dir, "%s.uniprot.json" % taxon)
with open(uniprot_json_file) as f:
uniaccs = json.load(f)
# For each UniProt Accession...
for uniacc in sorted(uniaccs):
# Skip if no sequence
if uniaccs[uniacc][1] is None: continue
# Digest to MD5
h = hashlib.new("md5")
h.update(uniaccs[uniacc][1].encode("utf-8"))
md5 = h.hexdigest() + uniaccs[uniacc][1][:4] + uniaccs[uniacc][1][-4:]
# If sequence in Cis-BP...
if md5 in cisbp:
# Add to domains
domains.setdefault(uniacc, [cisbp[md5][1], cisbp[md5][0]])
# For each profile...
for profile in uniaccs[uniacc][0]:
# Add to JASPAR
jaspar.setdefault(uniacc, [])
jaspar[uniacc].append([profile, profiles[profile]])
# Write
functions.write(domains_json_file, json.dumps(
domains, sort_keys=True, indent=4, separators=(",", ": ")))
functions.write(jaspar_json_file, json.dumps(
jaspar, sort_keys=True, indent=4, separators=(",", ": ")))
