def get_default_df(cls, usecache=True):
cp = ConfigParser()
cp.read(os.path.expanduser('~/git/cafa4/etc/cafa4.conf'))
upg = UniProt(cp)
df = upg.get_swissprot_df(usecache=usecache)
return df
def __init__(self, ):
self.uniprot = UniProt()
self.family_domains_columns = [
'comment(DOMAIN)', 'comment(SIMILARITY)', 'families',
'feature(COILED COIL)', 'feature(COMPOSITIONAL BIAS)',
'feature(DOMAIN EXTENT)', 'feature(MOTIF)', 'feature(REGION)',
'feature(REPEAT)', 'feature(ZINC FINGER)'
]
def create(cls, name, query, godag, verbose=True):
if verbose:
print(
'No data with name \'{}\' found. Downloading... (This may take a while)'
.format(name))
# download current GO DAG
r = requests.get('http://purl.obolibrary.org/obo/go/go-basic.obo',
allow_redirects=True)
with open(PATH + '/godag/' + name + '.obo', 'wb') as file:
file.write(r.content)
# setup UniProt API
up = UniProt()
up.settings.TIMEOUT = None
# load GO DAG
godag = GoDag(name=godag)
# download
result = up.search(query,
columns='id, sequence, go(molecular function)')
df = pd.read_csv(StringIO(result), delimiter='\t')
# filter go terms present in godag
df['Gene ontology (molecular function)'] = df[
'Gene ontology (molecular function)'].map(lambda labels: [
l for l in re.findall('GO:\d{7}', str(labels))
if l in godag.GODAG
])
df = df[df['Gene ontology (molecular function)'].map(
lambda l: len(l) > 0)]
# annotate full go
df['Gene ontology (molecular function)'] = df[
'Gene ontology (molecular function)'].map(
lambda labels: godag.get_go_lineage_of(labels))
# clean
df = cls.clean(df)
# save
df['labels'] = df.apply(lambda row: '; '.join(row['labels']), axis=1)
os.mkdir(PATH + '/datasets/' + name)
df.to_csv(PATH + '/datasets/' + name + '/data.csv', index=False)
with open(PATH + '/datasets/' + name + '/info.txt', 'w') as file:
file.write('Downloaded: {}'.format(date.today()))
if verbose: print('Raw data successfully downloaded.')
class ProteinIdentifier(object):
def __init__(self):
super().__init__()
self.seguid = seguid
self.uniprot = UniProt(verbose=False)
def sequence_from_uniprot(self, uniprot_ac):
"""Returns protein sequence from uniprot identifier"""
try:
return self.uniprot.get_fasta_sequence(uniprot_ac)
except ValueError:
return None
@staticmethod
def protein_identifier_resolver():
"""Returns protein sequence of a given identifier, using"""
pass # TODO
@staticmethod
def encode(sequence):
"""Protein seguid checksum based on amino-acid sequence"""
return str(self.seguid(sequence))
def get_uniprot_df(accList):
from bioservices.uniprot import UniProt #imports uniprot
u = UniProt(verbose=True)
df = u.get_df(accList)
return df
class UniProt(object):
'''
Aux info plugin.
Takes dataframe, extracts entry_ids, adds info from uniprot.
Returns modified dataframe.
'''
ASPECTMAP = {'C': 'cc', 'F': 'mf', 'P': 'bp'}
def __init__(self, config):
self.log = logging.getLogger(self.__class__.__name__)
self.config = config
self.uniprotapi = None
self.outdir = os.path.expanduser(config.get('global', 'outdir'))
self.taxid_mapfile = os.path.expanduser(
config.get('global', 'taxid_mapfile'))
self.sprotdatfile = os.path.expanduser(
config.get('ontologyplugin', 'sprotdatfile'))
self.cachedir = os.path.expanduser(
config.get('ontologyplugin', 'cachedir'))
excodes = config.get('ontologyplugin',
'excluded_evidence_codes',
fallback=[]).split(',')
excodes = [x.strip() for x in excodes]
self.excluded_evidence_codes = excodes
self.sprotdf = None
self.udf = None
self.tdf = pd.read_csv(self.taxid_mapfile, index_col=0)
# Create easy lookup mappings from taxon data frame...
itdf = self.tdf.set_index('taxonid')
self.taxiddict = itdf.to_dict(orient='index')
isdf = self.tdf.set_index('species')
self.specdict = isdf.to_dict(orient='index')
self.log.debug("UniProtGOlugin initialized.")
def cafa_execute(self, dataframe, online=False):
"""
Takes inbound dataframe of orthologs and adds in GO terms and evidence codes from
uniprot/swissprot.
For a given ortholog protein, one row is added for each GO term.
Returns new dataframe with all info.
"""
#
# inbound:
# cafaid evalue score bias db proteinacc protein species cafaprot cafaspec
# 0 T100900000001 1.100000e-156 523.6 8.5 sp Q9CQV8 1433B MOUSE 1433B MOUSE
# 1 T100900000001 4.100000e-155 518.4 7.7 sp P35213 1433B RAT 1433B MOUSE
# 2 T100900000001 5.400000e-155 518.0 7.2 sp A4K2U9 1433B PONAB 1433B MOUSE
# 3 T100900000001 5.400000e-155 518.0 7.2 sp P31946 1433B HUMAN 1433B MOUSE
# Get all unique target accession numbers.
entries = dataframe['proteinacc'].unique().tolist()
# Look up GOterms in uniprot...
if online:
self.uniprotapi = UniProt()
self.log.debug("Querying uniprot API for %d unique entries" %
len(entries))
self.udf = self.uniprotapi.get_df(entries)
self.log.debug(f"\n{self.udf}")
self.udf.to_csv("%s/uniprot.csv" % self.outdir)
udfslim = self.udf[['Entry', 'Gene ontology IDs']]
# df.tacc corresponds to udf.Entry ...
# entry == proteinid
# gene ontology id = goterm
#
self.log.debug("Making new rows for each goterm.")
newrowdict = {}
ix = 0
for row in udfslim.itertuples():
(entry, golist) = row[1:]
for goterm in golist:
#print("creating new row: %s : %s %s %s" % (ix, entry, gene, goterm))
newrow = [entry, goterm]
newrowdict[ix] = newrow
ix += 1
godf = pd.DataFrame.from_dict(newrowdict,
orient='index',
columns=['entry', 'goterm'])
else:
self.log.debug("Using offline functionality...")
godf = self.get_swissprot_df(usecache=True)
self.log.debug(f"GO DataFrame:\n{godf}")
# proteinid proteinacc goterm goaspect goevidence
# 0 001R_FRG3G Q6GZX4 GO:0046782 bp IEA
# 1 002L_FRG3G Q6GZX3 GO:0033644 cc IEA
# For each go term add row...
newdfdict = {}
ix = 0
for row in dataframe.itertuples():
self.log.debug("inbound row = %s" % str(row))
#(query, evalue, score, bias, db, tacc, protein, species) = row[1:]
(cafaid, evalue, score, bias, db, proteinacc, protein, species,
cafaprot, cafaspec) = row[1:]
self.log.debug(f"Searching for match for '{proteinacc}'")
gomatch = godf[godf.proteinacc == proteinacc]
self.log.debug(f"gomatch is:\n {gomatch}")
for gr in gomatch.itertuples():
(entry, proteinacc, protein, species, goterm, goaspect,
goevidence) = gr[1:]
newrow = [
cafaid, evalue, score, bias, db, proteinacc, protein,
species, cafaprot, cafaspec, goterm, goaspect, goevidence
]
newdfdict[ix] = newrow
ix += 1
newdf = pd.DataFrame.from_dict(newdfdict,
orient='index',
columns=[
'cafaid', 'evalue', 'score', 'bias',
'db', 'proteinacc', 'protein',
'species', 'cafaprot', 'cafaspec',
'goterm', 'goaspect', 'goevidence'
])
for xc in self.excluded_evidence_codes:
self.log.debug(
f"{len(newdf.index)} rows. Removing evidence code {xc}...")
#newdf = newdf[newdf.goevidence != xc]
newdf.drop(newdf.loc[newdf['goevidence'] == xc].index,
inplace=True)
self.log.debug(f"{len(newdf.index)} rows after.")
self.log.debug(f"\n{str(newdf)}")
return newdf
# Output:
# cafaid evalue score bias db proteinacc protein species cafaprot cafaspec goterm goaspect goevidence
# 0 T100900000001 1.100000e-156 523.6 8.5 sp Q9CQV8 1433B MOUSE 1433B MOUSE GO:0005737 cc ISO
# 1 T100900000001 1.100000e-156 523.6 8.5 sp Q9CQV8 1433B MOUSE 1433B MOUSE GO:0005829 cc ISO
# 2 T100900000001 1.100000e-156 523.6 8.5 sp Q9CQV8 1433B MOUSE 1433B MOUSE GO:0042470 cc IEA
#
def _dat2upr(self):
self.log.debug("opening swissprot dat file %s" % self.sprotdatfile)
rgen = SeqIO.parse(self.sprotdatfile, "swiss")
i = 0
uprlist = []
self.log.debug("Completed SeqIO.parse(). Handling records...")
for record in rgen:
upr = UniProtRecord(record)
uprlist.append(upr)
#print(record)
i += 1
if i % 10000 == 0:
self.log.debug("Handled %d records..." % i)
# break
self.log.debug("parsed dat file of %d records" % len(uprlist))
return uprlist
def get_annotation_df(self):
self.log.debug("opening swissprot dat file %s" % self.sprotdatfile)
rgen = SeqIO.parse(self.sprotdatfile, "swiss")
self.log.debug("rgen type is %s" % type(rgen))
#self.log.debug("Created generator with %d records" % len(rgen))
i = 0
alltuples = []
for record in rgen:
#print(record)
i += 1
if i % 1000 == 0:
self.log.debug("Handled %d records..." % i)
goterms = []
for xf in record.dbxrefs:
if xf.startswith("GO:"):
gt = xf[3:]
goterms.append(gt)
if len(goterms) > 0:
proteinid = record.id
protein = record.name
taxonid = record.annotations['ncbi_taxid'][0]
for gt in goterms:
t = (taxonid, proteinid, protein, gt)
alltuples.append(t)
# fan out over goterms
else:
# ignore un-annotated entries.
pass
if i >= 1000:
break
#self.log.debug("generated %d tuples" % len(alltuples))
self.log.debug(f"Generated { len(alltuples) } tuples")
df = pd.DataFrame(
alltuples, columns=['taxonid', 'proteinid', 'protein', 'goterm'])
return df
##########################################
#
# Non-cafalib usage (NOT using API)
#
##########################################
def get_swissprot_df(self, usecache=True):
"""
Get swissprot info as dataframe from files, without API, one row per GOterm.
Fields:
proteinid protein taxonid goterm goaspect goevidence
self.proteinid = record.id
self.proteinacc = record. ?
self.protein = record.name
self.goterms = []
for xf in record.dbxrefs:
if xf.startswith("GO:"):
gt = xf[3:]
self.goterms.append(gt)
self.accessions = record.annotations['accessions']
self.taxonid = record.annotations['ncbi_taxid'][0]
"""
cachepath = f"{self.cachedir}/sprotgolist.csv"
if usecache:
if os.path.exists(cachepath):
self.sprotdf = pd.read_csv(cachepath, index_col=0)
self.log.debug(f"Loaded dataframe from cache: {cachepath}")
if self.sprotdf is not None:
self.log.debug("Cache hit. Using DataFrame from cache...")
else:
self.log.debug("Getting dictionary list...")
dlist = self._handle_swissprot_file()
self.log.debug(
f"Got dict list of {len(dlist)} entries. Creating dataframe..."
)
self.sprotdf = pd.DataFrame(dlist)
#self.sprotdf.set_index('proteinacc', inplace = True)
self.log.debug(f"Made dataframe:\n {str(self.sprotdf)}")
self.log.info(f"Saving dataframe to cache file: {cachepath}")
self.sprotdf.to_csv(cachepath)
return self.sprotdf
def _handle_swissprot_file(self):
'''
Read uniprot_sprot.dat and return list of dicts of relevant fields.
'''
self.log.debug("Handling swissprot file...")
filehandle = None
try:
self.log.info(f"Opening file {self.sprotdatfile}")
filehandle = open(self.sprotdatfile, 'r')
self.log.debug("File opened. Parsing...")
dlist = self._parsefile(filehandle)
filehandle.close()
except FileNotFoundError:
self.log.error("No such file %s" % filename)
finally:
if filehandle is not None:
filehandle.close()
self.log.debug("Parsed data file.")
return dlist
def _parsefile(self, filehandle):
"""
Parses sprot DAT file and fans out goterms to list of dicts.
"""
allentries = []
current = None
sumreport = 1
suminterval = 10000
repthresh = sumreport * suminterval
try:
while True:
line = filehandle.readline()
if line == '':
break
#for line in filehandle:
if line.startswith("ID "):
# ID 001R_FRG3G Reviewed; 256 AA.
# <prot_name>_<prot_spec>
proteinid = line[5:16].strip()
current = defaultdict(dict)
current['proteinid'] = proteinid
(protein, species) = proteinid.split('_')
current['protein'] = protein
current['species'] = species
self.log.debug("Handling ID. New entry.")
elif line.startswith("AC "):
# AC Q6GZX4;
# AC Q91896; O57469;
self.log.debug("Handling AC.")
accession = line[5:11].strip()
current['proteinacc'] = accession
elif line.startswith("OX "):
#OX NCBI_TaxID=654924;
self.log.debug("Handling OX.")
taxonid = ""
val = line[5:]
fields = val.split('=')
if fields[0] == 'NCBI_TaxID':
taxonid = fields[1].strip().replace(';', '')
current['taxonid'] = taxonid
elif line.startswith("DR GO;"):
# DR GO; GO:0046782; P:regulation of viral transcription; IEA:InterPro.
# P biological process, C cellular component, F molecular function.
self.log.debug("Handling DR.")
fields = line.split(';')
goterm = fields[1].strip()
goinfo = fields[2]
aspcode = goinfo.split(':')[0].strip()
goaspect = UniProt.ASPECTMAP[aspcode]
goevsrc = fields[3]
(goevidence, evsrc) = goevsrc.split(':')
goevidence = goevidence.strip()
current['goterms'][goterm] = [goaspect, goevidence]
elif line.startswith("SQ SEQUENCE"):
self.log.debug("Handling SQ: XXX")
# line = filehandle.readline()
elif line.startswith("GN "):
# Examples:
# GN ABL1 {ECO:0000303|PubMed:21546455},
# GN Name=BRCA1; Synonyms=RNF53;
# GN ORFNames=T13E15.24/T13E15.23, T14P1.25/T14P1.24;
#
self.log.debug("Handling GN.")
val = line[5:]
elif line.startswith("//"):
self.log.debug("End of entry.")
clist = self._handle_current(current)
current = None
allentries.extend(clist)
self.log.debug(
f"All entries list now {len(allentries)} items... ")
if len(allentries) >= repthresh:
self.log.info(
f"Processed {len(allentries)} entries... ")
sumreport += 1
repthresh = sumreport * suminterval
except Exception as e:
traceback.print_exc(file=sys.stdout)
self.log.info(f"Parsed file with {len(allentries)} goterms")
return allentries
def _handle_current(self, currentinfo):
"""
takes dictionary:
currentinfo = { 'proteinid' : 'x', 'protein' : 'xxx' , 'goterms' : { 'GO:0005634' : [ 'C' , 'HDA' ],
'GO:0005886' : [ 'C' ,'HDA'],
}
}
returns list of dicts:
[ { 'proteinid' : 'x', 'protein' : 'xxx' , 'goterm' : 'GO:0005634',
'goaspect':'cc',
'goevidence': 'HDA' },
{ 'proteinid' : 'x', 'protein' : 'xxx' , 'goterm' : 'GO:0005886',
'goaspect':'cc',
'goevidence': 'HDA' },
]
"""
self.log.debug(f'handling {currentinfo} ')
newlist = []
gtdict = currentinfo['goterms']
for gt in gtdict.keys():
self.log.debug(f"Handling term {gt}")
newdict = {}
newdict['proteinid'] = currentinfo['proteinid']
newdict['proteinacc'] = currentinfo['proteinacc']
newdict['protein'] = currentinfo['protein']
newdict['species'] = currentinfo['species']
newdict['goterm'] = gt
newdict['goaspect'] = currentinfo['goterms'][gt][0]
newdict['goevidence'] = currentinfo['goterms'][gt][1]
newlist.append(newdict)
self.log.debug(f"Created fanout of length: {len(newlist)}")
return newlist
def _make_species_map(self):
'''
Parses uniprot speclist.txt https://www.uniprot.org/docs/speclist.txt
to local .CSV
taxonid species lineanname commonname
72259 ABANI Abaeis nicippe Sleepy orange butterfly
OXYMO E 475340: N=Oxytenis modestia
C=Costa Rica leaf moth
S=Dead-leaf moth
'''
listfile = self.speciesmap
self.log.debug("Opening species map file %s" % listfile)
try:
fh = open(listfile, 'r')
except FileNotFoundError:
self.log.error("No such file %s" % filename)
species = None
kingdom = None
taxonid = None
lineanname = None
commonname = None
columnnames = [
'species', 'kingdom', 'taxonid', 'lineanname', 'commonname'
]
datalist = []
# list of tuples
try:
for line in fh:
#self.log.debug("handling line %s" % line)
if 'N=' in line and not line.startswith('Code'):
#self.log.debug("handling N= line. taxonid is %s" % taxonid)
if species is not None:
tup = (species, kingdom, taxonid, lineanname,
commonname)
#self.log.debug("Adding tuple: %s" % str(tup))
datalist.append(tup)
# reset all varaiables
species = kingdom = taxonid = lineanname = commonname = None
species = line[:5]
kingdom = line[6]
taxonid = line[7:15].strip()
lineanname = line[19:].strip()
#self.log.debug("handling N= line. taxonid is %s" % taxonid)
elif 'C=' in line:
commonname = line[19:].strip()
elif 'S=' in line:
pass
except Exception as e:
traceback.print_exc(file=sys.stdout)
finally:
fh.close()
self.log.debug("Parsed file with %d terms" % len(datalist))
df = pd.DataFrame(datalist, columns=columnnames)
outfile = "%s/speclist.csv" % self.outdir
self.log.debug("Writing dataframe to %s" % outfile)
df.to_csv(outfile)
print(str(df))
return df
@classmethod
def get_default_df(cls, usecache=True):
cp = ConfigParser()
cp.read(os.path.expanduser('~/git/cafa4/etc/cafa4.conf'))
upg = UniProt(cp)
df = upg.get_swissprot_df(usecache=usecache)
return df
@classmethod
def calculate_prior(cls, dataframe, species=None, goaspect=None):
"""
@arg
dataframe : standard internal dataframe,
species : NCBI species code e.g. MOUSE | HUMAN
goaspect : internal aspect code e.g. [cc | bp | mf ]
proteinid proteinacc protein species goterm goaspect goevidence
11K_PAVHV P0DJZ0 11K PAVHV GO:0030430 cc IDA
...
returns:
dataframe w/ ranked list of goterms, within the specified species/aspect if supplied.
otherwise globally
goterm goaspect count prob
GO:0045735 cc 3679 .142
GO:0030433 bp 1256 .086
"""
df = dataframe
if species is not None:
df = df[df.species == species]
if goaspect is not None:
df = df[df.goaspect == goaspect]
totalterms = df.goterm.count()
newdf = pd.DataFrame(df.goterm.value_counts()).reset_index()
newdf.columns = ['goterm', 'counts']
from bioservices.uniprot import UniProt
import requests, json
from xml.etree import ElementTree
import xml.etree.ElementTree as ET
u = UniProt()
res = u.search('sphingolipid_metabolism+AND+organism:9606',
frmt='tab',
columns='id')
identifiers = res.strip().split()[1:]
#hey = open('iuphar.txt','w')
for line in identifiers:
url = "http://www.guidetopharmacology.org/services/targets?accession=%s&database=UniProt/XML" % line
response = requests.get(url)
t = response.status_code
r = response.content
if len(r) is not 0:
t = r.find('targetId')
a = r[t + 12] + r[t + 13] + r[t + 14] + r[t + 15]
url = "http://www.guidetopharmacology.org/services/targets/%s/rankOrder" % a
response = requests.get(url)
T = response.content
if len(T) is not 0:
s = T.find('id=')
oh = T[s + 3] + T[s + 4] + T[s + 5] + T[s + 6]
url = "http://www.guidetopharmacology.org/services/ligands/%s/structure" % oh
response = requests.get(url)
ligand = response.content
key = ligand.find('"smiles" :') + len('"smiles" :')
for i in range(30):
print ligand[key + i],
from pandas import Series, DataFrame
import pandas as pd
from bioservices.uniprot import UniProt
u = UniProt(verbose=False)
#filename= "~/YuLab/interlogs/HumanBinary_All.txt"
filename = "HumanBinary_All.txt"
def get_seq_ppi(filename):
"""Return all the items in the file named filename; if testfn
then include only those items for which testfn is true"""
with open(filename) as file:
#return get_pairs(file)
p = get_Ps(file)
pp = p[0]
ppid = get_ppi(pp)
return ppid
#def get_items
# def get_pairs(src):
# pairs = [[line.split()[0], line.split()[1]] for line in src if line[0] != '']
# for pp in pairs:
# k = (pp[0], pp[1])
# return k
def get_Ps(src):
class GeneVis:
def __init__(self, ):
self.uniprot = UniProt()
self.family_domains_columns = [
'comment(DOMAIN)', 'comment(SIMILARITY)', 'families',
'feature(COILED COIL)', 'feature(COMPOSITIONAL BIAS)',
'feature(DOMAIN EXTENT)', 'feature(MOTIF)', 'feature(REGION)',
'feature(REPEAT)', 'feature(ZINC FINGER)'
]
def ensembl2Uniprot(
self,
ensembl_txid,
):
d = u.mapping(fr="ENSEMBL_TRS_ID", to="ACC", query=ensembl_txid)
def search(self, uniprot_kw="Nid1_MOUSE"):
#for col in family_domains_columns:
results = self.uniprot.search(uniprot_kw,
columns=','.join(
self.family_domains_columns))
self._results = results
comm_pat = '(\d+)[.]+(\d+);[\t ]+/note=([0-9a-zA-Z"\- ]+);'
domain_pat = re.compile('DOMAIN ' + comm_pat)
motif_pat = re.compile('MOTIF ' + comm_pat)
repeat_pat = re.compile('REPEAT ' + comm_pat)
region_pat = re.compile('REGION ' + comm_pat)
temp = []
for pat in [domain_pat, motif_pat, repeat_pat, region_pat]:
## convert to pandas df
ext = pat.findall(results)
if ext:
temp += ext
temp2 = pd.DataFrame.from_records(temp,
columns=('start', 'end', 'group'))
temp2.insert(0, column='chromosome', value='1')
temp2.insert(3, column='strand', value=None)
temp2['group'] = temp2['group'].str.strip('"')
temp2['type'] = temp2['group'].str.replace(r" \d", "", regex=True)
temp2.start = temp2.start.astype(int)
temp2.end = temp2.end.astype(int)
if temp2.empty:
print(f"Warning: NO features found for {uniprot_kw}")
self.features = temp2
self._max_length = int(
self.uniprot.search(uniprot_kw, columns='length').split("\n")[1])
def show(self, region=None, show_label=False, figsize=(12, None)):
# Plot track.
feat_track = FeatureTrack(data=self.features,
hue='type',
label='group' if show_label else None)
if self.features.empty:
print("No found genes. do search again")
return
if region is None:
region = ('1', 0, self.features.end.max() + 1)
fig, ax = plot_tracks([feat_track],
region=region,
figsize=figsize,
despine=True)
#self.figure = fig
return ax
def add_mutation_feature(self, start, end, label, color="#FF1700"):
self._features.append(
GraphicFeature(start=start,
end=end,
strand=+1,
color=color,
label=label))
self._max_length = max(self._max_length, end)
def add_feature(self, palette='tab10'):
if self.features.empty:
print("No found genes. do search again")
return
self._features = []
ft = self.features['type'].unique()
colors = sns.color_palette(palette=palette, n_colors=len(ft)).as_hex()
self.features['color'] = self.features['type'].map(
{t: c
for t, c in zip(ft, colors)})
for i, row in self.features.iterrows():
f = GraphicFeature(start=row.start,
end=row.end,
strand=+1,
color=row.color,
label=row.group)
self._features.append(f)
def show_feature(self, figure_width=8, xlabel=""):
if len(self._features) < 1:
print("No feautres to show")
return
record = GraphicRecord(sequence_length=self._max_length,
features=self._features)
ax, _ = record.plot(figure_width=figure_width)
ax.set_xlabel(xlabel, fontweight="bold", fontsize=16)
return ax
def test_testset(config):
upg = UniProt(config)
df = upg.get_annotation_df()
return df
def test_speciesmap(config):
upg = UniProt(config)
upg._make_species_map()
def test_datparse(config):
upg = UniProt(config)
df = upg.get_swissprot_df()
return df
def test_uniprot(config):
upg = UniProt(config)
entrylist = ['Q9CQV8', 'P35213', 'A4K2U9', 'P31946', 'Q4R572', 'P68250']
out = upg._query_entries(entrylist)
print(out)
def cafa_execute(self, dataframe, online=False):
"""
Takes inbound dataframe of orthologs and adds in GO terms and evidence codes from
uniprot/swissprot.
For a given ortholog protein, one row is added for each GO term.
Returns new dataframe with all info.
"""
#
# inbound:
# cafaid evalue score bias db proteinacc protein species cafaprot cafaspec
# 0 T100900000001 1.100000e-156 523.6 8.5 sp Q9CQV8 1433B MOUSE 1433B MOUSE
# 1 T100900000001 4.100000e-155 518.4 7.7 sp P35213 1433B RAT 1433B MOUSE
# 2 T100900000001 5.400000e-155 518.0 7.2 sp A4K2U9 1433B PONAB 1433B MOUSE
# 3 T100900000001 5.400000e-155 518.0 7.2 sp P31946 1433B HUMAN 1433B MOUSE
# Get all unique target accession numbers.
entries = dataframe['proteinacc'].unique().tolist()
# Look up GOterms in uniprot...
if online:
self.uniprotapi = UniProt()
self.log.debug("Querying uniprot API for %d unique entries" %
len(entries))
self.udf = self.uniprotapi.get_df(entries)
self.log.debug(f"\n{self.udf}")
self.udf.to_csv("%s/uniprot.csv" % self.outdir)
udfslim = self.udf[['Entry', 'Gene ontology IDs']]
# df.tacc corresponds to udf.Entry ...
# entry == proteinid
# gene ontology id = goterm
#
self.log.debug("Making new rows for each goterm.")
newrowdict = {}
ix = 0
for row in udfslim.itertuples():
(entry, golist) = row[1:]
for goterm in golist:
#print("creating new row: %s : %s %s %s" % (ix, entry, gene, goterm))
newrow = [entry, goterm]
newrowdict[ix] = newrow
ix += 1
godf = pd.DataFrame.from_dict(newrowdict,
orient='index',
columns=['entry', 'goterm'])
else:
self.log.debug("Using offline functionality...")
godf = self.get_swissprot_df(usecache=True)
self.log.debug(f"GO DataFrame:\n{godf}")
# proteinid proteinacc goterm goaspect goevidence
# 0 001R_FRG3G Q6GZX4 GO:0046782 bp IEA
# 1 002L_FRG3G Q6GZX3 GO:0033644 cc IEA
# For each go term add row...
newdfdict = {}
ix = 0
for row in dataframe.itertuples():
self.log.debug("inbound row = %s" % str(row))
#(query, evalue, score, bias, db, tacc, protein, species) = row[1:]
(cafaid, evalue, score, bias, db, proteinacc, protein, species,
cafaprot, cafaspec) = row[1:]
self.log.debug(f"Searching for match for '{proteinacc}'")
gomatch = godf[godf.proteinacc == proteinacc]
self.log.debug(f"gomatch is:\n {gomatch}")
for gr in gomatch.itertuples():
(entry, proteinacc, protein, species, goterm, goaspect,
goevidence) = gr[1:]
newrow = [
cafaid, evalue, score, bias, db, proteinacc, protein,
species, cafaprot, cafaspec, goterm, goaspect, goevidence
]
newdfdict[ix] = newrow
ix += 1
newdf = pd.DataFrame.from_dict(newdfdict,
orient='index',
columns=[
'cafaid', 'evalue', 'score', 'bias',
'db', 'proteinacc', 'protein',
'species', 'cafaprot', 'cafaspec',
'goterm', 'goaspect', 'goevidence'
])
for xc in self.excluded_evidence_codes:
self.log.debug(
f"{len(newdf.index)} rows. Removing evidence code {xc}...")
#newdf = newdf[newdf.goevidence != xc]
newdf.drop(newdf.loc[newdf['goevidence'] == xc].index,
inplace=True)
self.log.debug(f"{len(newdf.index)} rows after.")
self.log.debug(f"\n{str(newdf)}")
return newdf
def __init__(self):
super().__init__()
self.seguid = seguid
self.uniprot = UniProt(verbose=False)
def uniprot():
u = UniProt(verbose=False, cache=False)
u.debugLevel = "ERROR"
return u
def test_swissprot(config):
logging.debug("Running test_swissprot")
upg = UniProt(config)
out = upg.get_swissprot_df()
print(str(out))
import json
import requests
import tempfile
import ssbio.databases.pdb
import ssbio.utils
import os.path as op
from bioservices.uniprot import UniProt
import ssbio.databases.uniprot
bs_unip = UniProt()
def get_pdbs_for_gene(bigg_model, bigg_gene, cache_dir=tempfile.gettempdir()):
"""Attempt to get a rank-ordered list of available PDB structures for a BiGG Model and its gene.
Args:
bigg_model: BiGG Model ID
bigg_gene: BiGG Gene ID
Returns:
list: rank-ordered list of tuples of (pdb_id, chain_id)
"""
my_structures = []
# Download gene info
gene = ssbio.utils.request_json(link='http://bigg.ucsd.edu/api/v2/models/{}/genes/{}'.format(bigg_model, bigg_gene),
outfile='{}_{}.json'.format(bigg_model, bigg_gene),
outdir=cache_dir,
force_rerun_flag=False)
uniprots = []
""" Since BindingDB has its own monomer IDs, all IDs are converted to PubChem CIDs. For that, the list of all the identifier
mappings from monomer ID to PubChem IDs is downloaded from BindingDB webpage given below. That the file called monomer.txt
is used in the code. Thus, used need to download the updated list, then use it in our code.
(https://www.bindingdb.org/bind/chemsearch/marvin/SDFdownload.jsp?all_download=yes)"""
from bioservices.uniprot import UniProt
import requests
from xml.etree import ElementTree
u = UniProt()
res = u.search('(sphingolipid+OR+sphingomyelin+OR+glycosphingolipid)+AND+organism:9606 ', frmt='tab',columns='id')
identifiers = res.strip().split()[1:]
#hey = open("bindingdb.txt","w")
f=open("monomer.txt","r")
lines=f.readlines()
monoid = []
mono = []
sim= []
CID=[]
cid = []
""" All the monomerIDs and their equivalent CIDs are saved as separate arrays"""
for line in lines:
monoid.append(line.split()[0])
for line in lines:
cid.append(line.split()[1])
hagaiNames = [
"Microenvironment_ID", "Binding_motif", "Cofactor", "Metal",
"cofactor_group", "EC", "Head", "Molecule", "Organism_scientific",
"no_rank", "superkingdom", "phylum", "class_", "order", "family", "genus",
"organism_taxid", "name", "chains", "Resolution", "Structure_method",
"Keywords", "Journal_reference", "Release_date"
]
dfHag = pd.read_csv(os.path.join(hdir, 'hagai.csv'), header=0, index_col=False)
dfHag[['pdb', 'LIG', 'chain', 'resID',
'function']] = dfHag.Microenvironment_ID.str.split('[._]', expand=True)
dfHag['resID'] = dfHag.resID.astype(int)
dfHag['Binding_motif'] = dfHag.Binding_motif.astype(int)
dfHag['hagai'] = 'yes'
import numpy as np
dfHag['ec'] = np.nan
u = UniProt(verbose=True)
bar = Bar("Processing",
max=len(dfHag.index),
fill='*',
suffix='%(percent).1f%% - %(eta)ds')
map = u.mapping('PDB_ID', 'ACC', query=dfHag.pdb)
# print(map)
# exit()
df = u.get_df([id[0] for id in map.values()])
df.to_csv(os.path.join(hdir, 'df_microPDBs.csv')) #returns dataframe with
# Unnamed: 0
# Entry
# Entry name Gene names Gene names (primary ) Gene names (synonym ) Gene names (ordered locus )
# Gene names (ORF ) Organism Organism ID
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 9 11:46:12 2016
@author: ewj
"""
from Bio import SeqIO
import myUniprotIO
from UniprotUtils import get_feature_frame
from bioservices.uniprot import UniProt
u = UniProt(verbose = True)
import pandas as pd
from tqdm import tqdm
import os, itertools
def evidence(feature,letter,out_file):
#read query file
x = myUniprotIO.UniprotIterator(open('query.xml','r'), return_raw_comments=True)
#parse for wanted data (i.e. gene name, sequence id, position, etc.)
L = []
for rec,seqrec in tqdm(enumerate(x)):
gene_name = seqrec.annotations.get('gene_name_primary','_none_')
t= (
get_feature_frame(seqrec,stype=feature,filter_val=letter)
.assign(rec=rec, id=seqrec.id, gene_name=gene_name)
.rename(columns={'start':'position'})
)
L.append(t)
import re
blast = open("staph_out.txt", 'r')
table = defaultdict(int)
for line in blast:
match = re.search("\A> \w", line)
if (match):
match = re.search("\w{,5}_\w{,5}\s", line[2:])
if (match):
table[match.group()] += 1
blast.close()
print(len(table))
blastOut = open("blast.tsv", 'w')
u = UniProt(verbose=False)
goTable = defaultdict(int)
i = 0
for item in table:
blastOut.write(item + '\t' + str(table[item]) + '\n')
i += 1
if (i % 25 == 0):
print(i)
value = u.search(item, columns="go")
value = value.split(';')
for val in value:
match = re.search("GO:\d*", val)
if (match):
goTable[match.group()] += (1 * table[item])
blastOut.close()
def uniprot():
u = UniProt(verbose=False, cache=False)
u.logging.level = "ERROR"
return u