def download_proteins(proteins, data_dir, fileroot="uniprot"):
"""
Given a list of proteins, download their sequences to a FASTA file.
Parameters
----------
proteins : Tuple[str]
Uniprot accessions to retrieve
data_dir : str
Where to download the FASTA file.
fileroot : str
How should the file be named?
Returns
-------
str
The FASTA file created.
"""
uniprot = bioservices.UniProt()
outfile = os.path.join(data_dir, fileroot + ".fasta")
with open(outfile, "w") as fasta_out:
lines = uniprot.retrieve(proteins, frmt="fasta")
lines = "".join(lines)
fasta_out.write(lines)
return outfile
def resolveAnnotationHelper(annotation):
if not hasattr(resolveAnnotation, "db"):
resolveAnnotation.db = {}
resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
resolveAnnotation.uni = bioservices.UniProt(verbose=False)
resolveAnnotation.k = bioservices.kegg.KEGG(verbose=False)
resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
resolveAnnotation.t = bioservices.Taxon()
resolveAnnotation.db[
"http://identifiers.org/uniprot/P62988"
] = "http://identifiers.org/uniprot/P62988"
resolveAnnotation.db[
"http://identifiers.org/uniprot/P06842"
] = "http://identifiers.org/uniprot/P06842"
resolveAnnotation.db[
"http://identifiers.org/uniprot/P07006"
] = "http://identifiers.org/uniprot/P06842"
if annotation in resolveAnnotation.db:
return annotation, resolveAnnotation.db[annotation]
tAnnotation = annotation.replace("%3A", ":")
tAnnotation = annotation.split("/")[-1]
# tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
try:
if "obo.go" in annotation or "/go/GO" in annotation:
res = resolveAnnotation.qg.Term(tAnnotation)
finalArray = []
if type(res) not in [int]:
res = bioservices.Service("name").easyXML(res)
tmp = res.findAll("name")
for x in tmp:
try:
tagString = str(goGrammar.parseString(str(x))[0])
if tagString not in ["Systematic synonym"]:
finalArray.append(str(goGrammar.parseString(str(x))[0]))
except pyp.ParseBaseException:
continue
if len(finalArray) > 0:
resolveAnnotation.db[annotation] = finalArray[0]
else:
resolveAnnotation.db[annotation] = ""
finalAnnotation = resolveAnnotation.db[annotation]
elif "kegg" in annotation:
data = resolveAnnotation.k.get(tAnnotation)
dict_data = resolveAnnotation.k.parse(data)
if type(dict_data) == int:
resolveAnnotation.db[annotation] = ""
else:
resolveAnnotation.db[annotation] = dict_data["name"]
finalAnnotation = resolveAnnotation.db[annotation]
elif "uniprot" in annotation:
identifier = annotation.split("/")[-1]
result = resolveAnnotation.uni.quick_search(identifier)
if identifier in result:
resolveAnnotation.db[annotation] = result[identifier][
"Protein names"
].split("(")[0]
else:
finalAnnotation = ""
finalAnnotation = resolveAnnotation.db[annotation]
elif "chebi" in annotation:
tmp = annotation.split("/")[-1]
entry = resolveAnnotation.ch.getLiteEntity(tmp)
finalAnnotation = ""
for element in entry:
resolveAnnotation.db[annotation] = str(element["chebiAsciiName"])
finalAnnotation = resolveAnnotation.db[annotation]
elif (
"cco" in annotation
or "pirsf" in annotation
or "pubchem" in annotation
or "omim" in annotation
):
finalAnnotation = ""
elif "taxonomy" in annotation:
# uniprot stuff for taxonomy
result = resolveAnnotation.t.search_by_taxon(tAnnotation)
resolveAnnotation.db[annotation] = result["Scientific Name"]
finalAnnotation = resolveAnnotation.db[annotation]
"""
url = 'http://www.uniprot.org/taxonomy/'
params = {
'from':'ACC',
'to':'P_REFSEQ_AC',
'format':'tab',
'query':'P13368 P20806 Q9UM73 P97793 Q17192'
}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
"""
else:
return annotation, ""
# assert(False)
finalAnnotation = ""
except (IOError, KeyError) as e:
return annotation, ""
return annotation, finalAnnotation
def resolveAnnotationHelper(annotation):
if not hasattr(resolveAnnotation, 'db'):
resolveAnnotation.db = {}
resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
resolveAnnotation.uni = bioservices.UniProt(verbose=False)
resolveAnnotation.k = bioservices.kegg.KEGG(verbose=False)
resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
resolveAnnotation.t = bioservices.Taxon()
resolveAnnotation.db[
'http://identifiers.org/uniprot/P62988'] = 'http://identifiers.org/uniprot/P62988'
resolveAnnotation.db[
'http://identifiers.org/uniprot/P06842'] = 'http://identifiers.org/uniprot/P06842'
resolveAnnotation.db[
'http://identifiers.org/uniprot/P07006'] = 'http://identifiers.org/uniprot/P06842'
if annotation in resolveAnnotation.db:
return annotation, resolveAnnotation.db[annotation]
tAnnotation = annotation.replace('%3A', ':')
tAnnotation = annotation.split('/')[-1]
#tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
try:
if 'obo.go' in annotation or '/go/GO' in annotation:
res = resolveAnnotation.qg.Term(tAnnotation)
finalArray = []
if type(res) not in [int]:
res = bioservices.Service('name').easyXML(res)
tmp = res.findAll('name')
for x in tmp:
try:
tagString = str(goGrammar.parseString(str(x))[0])
if tagString not in ['Systematic synonym']:
finalArray.append(
str(goGrammar.parseString(str(x))[0]))
except pyp.ParseBaseException:
continue
if len(finalArray) > 0:
resolveAnnotation.db[annotation] = finalArray[0]
else:
resolveAnnotation.db[annotation] = ''
finalAnnotation = resolveAnnotation.db[annotation]
elif 'kegg' in annotation:
data = resolveAnnotation.k.get(tAnnotation)
dict_data = resolveAnnotation.k.parse(data)
if type(dict_data) == int:
resolveAnnotation.db[annotation] = ''
else:
resolveAnnotation.db[annotation] = dict_data['name']
finalAnnotation = resolveAnnotation.db[annotation]
elif 'uniprot' in annotation:
identifier = annotation.split('/')[-1]
result = resolveAnnotation.uni.quick_search(identifier)
if identifier in result:
resolveAnnotation.db[annotation] = result[identifier][
'Protein names'].split('(')[0]
else:
finalAnnotation = ''
finalAnnotation = resolveAnnotation.db[annotation]
elif 'chebi' in annotation:
tmp = annotation.split('/')[-1]
entry = resolveAnnotation.ch.getLiteEntity(tmp)
finalAnnotation = ''
for element in entry:
resolveAnnotation.db[annotation] = str(
element['chebiAsciiName'])
finalAnnotation = resolveAnnotation.db[annotation]
elif 'cco' in annotation or 'pirsf' in annotation or 'pubchem' in annotation or 'omim' in annotation:
finalAnnotation = ''
elif 'taxonomy' in annotation:
#uniprot stuff for taxonomy
result = resolveAnnotation.t.search_by_taxon(tAnnotation)
resolveAnnotation.db[annotation] = result['Scientific Name']
finalAnnotation = resolveAnnotation.db[annotation]
'''
url = 'http://www.uniprot.org/taxonomy/'
params = {
'from':'ACC',
'to':'P_REFSEQ_AC',
'format':'tab',
'query':'P13368 P20806 Q9UM73 P97793 Q17192'
}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
'''
else:
return annotation, ''
#assert(False)
finalAnnotation = ''
except (IOError, KeyError) as e:
return annotation, ''
return annotation, finalAnnotation