def __init__(self, UniProtAC, XML = None, cache_dir = None, silent = True):
if cache_dir and not(os.path.exists(cache_dir)):
raise Exception("The cache directory %s does not exist." % cache_dir)
self.UniProtAC = UniProtAC
self.silent = silent
# Get XML
if XML == None:
protein_xml = None
cached_filepath = None
if cache_dir:
cached_filepath = os.path.join(cache_dir, '%s.xml' % UniProtAC)
if cached_filepath and os.path.exists(cached_filepath):
protein_xml = read_file(cached_filepath)
else:
if not silent:
colortext.write("Retrieving %s\n" % UniProtAC, "cyan")
url = 'http://www.uniprot.org/uniprot/%s.xml' % UniProtAC
protein_xml = http_get(url)
if not(protein_xml.strip()):
raise EmptyUniProtACXMLException('The file %s is empty.' % UniProtAC)
if cached_filepath:
write_file(cached_filepath, protein_xml)
self.XML = protein_xml
else:
self.XML = XML
self.recommended_name = None
self.submitted_names = []
self.alternative_names = []
# Get DOM
try:
self._dom = parseString(protein_xml)
except:
if cached_filepath:
raise Exception("The UniProtAC XML for '%s' was invalid. The cached file is located at %s. Check this file - if it is not valid XML then delete the file and rerun the script." % (UniProtAC, cached_filepath))
else:
raise Exception("The UniProtAC XML for '%s' was invalid." % UniProtAC)
main_tags = self._dom.getElementsByTagName("uniprot")
assert(len(main_tags) == 1)
entry_tags = main_tags[0].getElementsByTagName("entry")
assert(len(entry_tags) == 1)
self.entry_tag = entry_tags[0]
self._parse_evidence_tag()
self._parse_sequence_tag()
self._parse_protein_tag()
self._parse_organism_tag()
self._parse_subsections()
self._parse_PDB_mapping()
def get_obsolete_acc_to_uniparc(acc):
''' Tries to determine the UniParc ID for obsolete ACCs which are not returned using uniprot_map.
:param acc: The UniProt accession number.
:return: The corresponding UniParc ID.
Warning: This is a fragile function as the underlying website generation or URL could change.
'''
contents = http_get('www.uniprot.org/uniparc/?query={0}'.format(acc))
mtchs = re.findall(r'"UPI[A-Z0-9]+?"', contents, re.DOTALL)
uniparc_id = set([m[1:-1] for m in mtchs])
if len(uniparc_id) == 1:
return uniparc_id.pop()
elif len(uniparc_id) > 1:
raise Exception('Multiple UPI identifiers found.')
return None
def _get_XML(self):
uparc_xml = None
cached_filepath = None
if self.cache_dir:
cached_filepath = os.path.join(self.cache_dir, '%s.xml' % self.UniParcID)
if cached_filepath and os.path.exists(cached_filepath):
uparc_xml = read_file(cached_filepath)
else:
if not self.silent:
colortext.write("Retrieving %s\n" % self.UniParcID, "cyan")
url = 'http://www.uniprot.org/uniparc/%s.xml' % self.UniParcID
uparc_xml = http_get(url)
if cached_filepath:
write_file(cached_filepath, uparc_xml)
self.XML = uparc_xml
# Get DOM
self._dom = parseString(uparc_xml)
main_tags = self._dom.getElementsByTagName("uniparc")
assert(len(main_tags) == 1)
entry_tags = main_tags[0].getElementsByTagName("entry")
assert(len(entry_tags) == 1)
self.entry_tag = entry_tags[0]
def __init__(self, UniParcID, UniProtACs = None, UniProtIDs = None, cache_dir = None, silent = False):
if cache_dir and not(os.path.exists(os.path.abspath(cache_dir))):
raise Exception("The cache directory %s does not exist." % os.path.abspath(cache_dir))
self.UniParcID = UniParcID
self.cache_dir = cache_dir
self.recommended_name = None
self.silent = silent
# Get AC mapping
if not UniProtACs or UniParcID=='UPI0000047CA3': # todo: is this UPI0000047CA3 special handling necessary?
mapping = uniprot_map('UPARC', 'ACC', [UniParcID], cache_dir = cache_dir, silent = silent)[UniParcID]
self.UniProtACs = mapping
else:
self.UniProtACs = UniProtACs
# Get ID mapping
if not UniProtIDs:
mapping = uniprot_map('UPARC', 'ID', [UniParcID], cache_dir = cache_dir, silent = silent)[UniParcID]
self.UniProtIDs = mapping
else:
self.UniProtIDs = UniProtIDs
# Get FASTA
cached_filepath = None
if cache_dir:
cached_filepath = os.path.join(cache_dir, '%s.fasta' % UniParcID)
if cached_filepath and os.path.exists(cached_filepath):
fasta = read_file(cached_filepath)
else:
if not silent:
print("Getting FASTA file")
url = 'http://www.uniprot.org/uniparc/%s.fasta' % UniParcID
fasta = http_get(url)
if cached_filepath:
write_file(cached_filepath, fasta)
# Get sequence
header = fasta.split("\n")[0].split()
assert(len(header) == 2)
assert(header[0] == ">%s" % UniParcID)
assert(header[1].startswith("status="))
sequence = "".join(map(string.strip, fasta.split("\n")[1:]))
self.sequence = sequence
# Get atomic mass (and sequence again)
self.atomic_mass = None
self.CRC64Digest = None
recommended_names = []
alternative_names = []
submitted_names = []
self.AC_entries = {}
subsections = ProteinSubsectionHolder(len(sequence))
for UniProtAC in self.UniProtACs:
#colortext.write("%s\n" % UniProtAC, 'cyan')
try:
AC_entry = UniProtACEntry(UniProtAC, cache_dir = self.cache_dir, silent = silent)
except EmptyUniProtACXMLException:
continue
self.AC_entries[UniProtAC] = AC_entry
# Mass sanity check
if self.atomic_mass != None:
assert(self.atomic_mass == AC_entry.atomic_mass)
self.atomic_mass = AC_entry.atomic_mass
# Sequence sanity check
assert(self.sequence == AC_entry.sequence)
# CRC 64 sanity check
if self.CRC64Digest != None:
assert(self.CRC64Digest == AC_entry.CRC64Digest)
self.CRC64Digest = AC_entry.CRC64Digest
assert(CRC64.CRC64digest(self.sequence) == self.CRC64Digest)
if AC_entry.recommended_name:
found = False
for n in recommended_names:
if n[0] == AC_entry.recommended_name:
n[1] += 1
found = True
break
if not found:
recommended_names.append([AC_entry.recommended_name, 1])
for alternative_name in AC_entry.alternative_names:
found = False
for n in alternative_names:
if n[0] == alternative_name:
n[1] += 1
found = True
break
if not found:
alternative_names.append([alternative_name, 1])
for submitted_name in AC_entry.submitted_names:
found = False
for n in submitted_names:
if n[0] == submitted_name:
n[1] += 1
found = True
break
if not found:
submitted_names.append([submitted_name, 1])
subsections += AC_entry.subsections
self.subsections = subsections
assert(len(set(UniParcMergedRecommendedNamesRemap.keys()).intersection(set(UniParcMergedSubmittedNamesRemap.keys()))) == 0)
if UniParcID in UniParcMergedRecommendedNamesRemap:
recommended_names = [[UniParcMergedRecommendedNamesRemap[UniParcID], 1]]
elif UniParcID in UniParcMergedSubmittedNamesRemap:
recommended_names = [[UniParcMergedSubmittedNamesRemap[UniParcID], 1]]
if not silent:
colortext.write('Subsections\n', 'orange')
#print(subsections)
if len(recommended_names) == 0 and len(alternative_names) == 0 and len(submitted_names) == 0:
raise UniParcEntryStandardizationException("UniParcID %s has no recommended names." % UniParcID)
elif len(recommended_names) == 0:
s = ["UniParcID %s has no recommended names.\n" % UniParcID]
if alternative_names:
s.append("It has the following alternative names:")
for tpl in sorted(alternative_names, key=lambda x:-x[1]):
s.append("\n count=%s: %s" % (str(tpl[1]).ljust(5), tpl[0]['Name']))
if tpl[0]['Short names']:
s.append(" (short names: %s)" % ",".join(tpl[0]['Short names']))
if tpl[0]['EC numbers']:
s.append(" (EC numbers: %s)" % ",".join(tpl[0]['EC numbers']))
if submitted_names:
s.append("It has the following submitted names:")
for tpl in sorted(submitted_names, key=lambda x:-x[1]):
s.append("\n count=%s: %s" % (str(tpl[1]).ljust(5), tpl[0]['Name']))
if tpl[0]['Short names']:
s.append(" (short names: %s)" % ",".join(tpl[0]['Short names']))
if tpl[0]['EC numbers']:
s.append(" (EC numbers: %s)" % ",".join(tpl[0]['EC numbers']))
#raise UniParcEntryStandardizationException("".join(s))
elif len(recommended_names) > 1:
s = ["UniParcID %s has multiple recommended names: " % UniParcID]
for tpl in sorted(recommended_names, key=lambda x:-x[1]):
s.append("\n count=%s: %s" % (str(tpl[1]).ljust(5), tpl[0]['Name']))
if tpl[0]['Short names']:
s.append(" (short names: %s)" % ",".join(tpl[0]['Short names']))
if tpl[0]['EC numbers']:
s.append(" (EC numbers: %s)" % ",".join(tpl[0]['EC numbers']))
raise UniParcEntryStandardizationException("".join(s))
#assert(len(recommended_names) == 1) # todo: this is not always available
#print(recommended_names)
self.recommended_name = None
if len(recommended_names) == 1:
self.recommended_name = recommended_names[0][0]
self.get_organisms()
