def toplist(self,
length=None,
alpha=None,
significant=True,
min_set_size=0,
groups=None,
filtr=lambda x: True,
**kwargs):
args = get_args(locals(), ['filtr', 'groups'])
if groups is None:
groups = self.gsea.groups.keys() # all by default
sets = set(
common.flat_list(s for g, s in iteritems(self.gsea.groups)
if g in groups))
return super(GSEABinaryEnrichmentSet, self).toplist(
filtr=lambda x: x[0] in sets and filtr(x), **args)
def kegg_interactions():
"""
Downloads and processes KEGG Pathways.
Returns list of interactions.
"""
rehsa = re.compile(r'.*(hsa[0-9]+).*')
req_hdrs = [
'Referer: http://www.genome.jp/kegg-bin/show_pathway'
'?map=hsa04710&show_description=show'
]
hsa_list = []
interactions = []
c = curl.Curl(urls.urls['kegg_pws']['list_url'], silent = True)
htmllst = c.result
lstsoup = bs4.BeautifulSoup(htmllst, 'html.parser')
for a in lstsoup.find_all('a', href = True):
m = rehsa.match(a['href'])
if m:
hsa_list.append((m.groups(0)[0], a.text))
prg = progress.Progress(
len(hsa_list), 'Processing KEGG Pathways', 1, percent = False)
for hsa, pw in hsa_list:
prg.step()
c = curl.Curl(urls.urls['kegg_pws']['kgml_url_2'] % hsa,
silent = True,
req_headers = req_hdrs)
kgml = c.result
kgmlsoup = bs4.BeautifulSoup(kgml, 'html.parser')
entries = {}
for ent in kgmlsoup.find_all('entry'):
gr = ent.find('graphics')
if gr and 'name' in gr.attrs:
entries[ent.attrs['id']] = [
n.strip()
for n in gr.attrs['name'].replace('...', '').split(',')
]
uentries = dict([(eid, common.uniq_list(
common.flat_list([
mapping.map_name(
gn, 'genesymbol', 'uniprot', strict = True) for gn in gns
]))) for eid, gns in iteritems(entries)])
for rel in kgmlsoup.find_all('relation'):
st = rel.find('subtype')
if (
rel.attrs['entry1'] in uentries and
rel.attrs['entry2'] in uentries and
st and
'name' in st.attrs
):
for u1 in uentries[rel.attrs['entry1']]:
for u2 in uentries[rel.attrs['entry2']]:
interactions.append((u1, u2, st.attrs['name'], pw))
prg.terminate()
return common.uniq_list(interactions)
def kegg_interactions():
"""
Downloads and processes KEGG Pathways.
Returns list of interactions.
"""
positive_terms = {'activation', 'expression'}
negative_terms = {'inhibition', 'repression'}
transc_terms = {'expression', 'repression'}
mechanism_terms = {
'phosphorylation',
'binding/association',
'dissociation',
'ubiquitination',
'dephosphorylation',
'glycosylation',
'state change',
'methylation',
}
direct_terms = {'indirect effect'}
KeggInteraction = collections.namedtuple(
'KeggInteraction',
[
'id_a',
'id_b',
'effect',
'pathway',
'mechanism',
'is_direct',
'transcriptional',
],
)
rehsa = re.compile(r'.*(hsa[0-9]+).*')
req_hdrs = [
'Referer: http://www.genome.jp/kegg-bin/show_pathway'
'?map=hsa04710&show_description=show'
]
hsa_list = []
interactions = []
c = curl.Curl(urls.urls['kegg_pws']['list_url'], silent=True)
htmllst = c.result
lstsoup = bs4.BeautifulSoup(htmllst, 'html.parser')
for a in lstsoup.find_all('a', href=True):
m = rehsa.match(a['href'])
if m:
hsa_list.append((m.groups(0)[0], a.text))
prg = progress.Progress(len(hsa_list),
'Processing KEGG Pathways',
1,
percent=False)
for hsa, pw in hsa_list:
prg.step()
c = curl.Curl(urls.urls['kegg_pws']['kgml_url_2'] % hsa,
silent=True,
req_headers=req_hdrs)
kgml = c.result
kgmlsoup = bs4.BeautifulSoup(kgml, 'html.parser')
entries = {}
for ent in kgmlsoup.find_all('entry'):
gr = ent.find('graphics')
if gr and 'name' in gr.attrs:
entries[ent.attrs['id']] = [
n.strip()
for n in gr.attrs['name'].replace('...', '').split(',')
]
uentries = dict([(eid,
common.uniq_list(
common.flat_list([
mapping.map_name(gn,
'genesymbol',
'uniprot',
strict=True) for gn in gns
]))) for eid, gns in iteritems(entries)])
for rel in kgmlsoup.find_all('relation'):
subtypes = {st.attrs['name'] for st in rel.find_all('subtype')}
if (rel.attrs['entry1'] in uentries
and rel.attrs['entry2'] in uentries and subtypes):
is_direct = 'indirect effect' not in subtypes
effect = ('inhibition' if negative_terms
& subtypes else 'activation' if positive_terms
& subtypes else 'unknown')
mechanism = ';'.join(mechanism_terms & subtypes)
transcriptional = bool(transc_terms & subtypes)
for u1 in uentries[rel.attrs['entry1']]:
for u2 in uentries[rel.attrs['entry2']]:
interactions.append(
KeggInteraction(
id_a=u1,
id_b=u2,
effect=effect,
pathway=pw,
mechanism=mechanism,
is_direct=is_direct,
transcriptional=transcriptional,
))
prg.terminate()
return common.uniq_list(interactions)
def get_pubmed_data(pp, cachefile=None, htp_threshold=20):
"""
For one PyPath object, obtains metadata for all PubMed IDs
through NCBI E-utils.
:param pp:
``pypath.PyPath`` object
:param htp_threshold:
The number of interactions for one reference
above the study considered to be high-throughput.
"""
if cachefile is None:
cachefile = settings.get('pubmed_cache')
if htp_threshold is not None:
pp.htp_stats()
pubmeds = common.uniq_list(
common.flat_list([[r.pmid for r in e['references']]
for e in pp.graph.es]))
if htp_threshold is not None:
pubmeds = set(pubmeds) - pp.htp[htp_threshold]['htrefs']
notpmid = [i for i in pubmeds if not i.isdigit()]
sys.stdout.write('\t:: Number of non PubMed ID references: %u\n' %
len(notpmid))
pmdata = {}
if os.path.exists(cachefile):
sys.stdout.write('\t:: Loading data previously downloaded '
'from PubMed, from file `%s`\n' % cachefile)
pmdata = pickle.load(open(cachefile, 'rb'))
missing = list(set(pubmeds) - set(pmdata.keys()))
sys.stdout.write('\t:: Downloading data from PubMed about %s papers\n' %
len(missing))
cached_pubmeds_len = len(pmdata)
pmdata_new = pubmed_input.get_pubmeds(missing)
pmdata.update(pmdata_new)
sys.stdout.write('\t:: Saving PubMed data to file `%s`\n' % cachefile)
if len(pmdata) > cached_pubmeds_len:
pickle.dump(pmdata, open(cachefile, 'wb'))
pmdata = dict(i for i in pmdata.items() if i[0] in pubmeds)
points = []
earliest = []
for e in pp.graph.es:
for s, rs in iteritems(e['refs_by_source']):
pms = [
r.pmid for r in rs
if (htp_threshold is None
or r.pmid not in pp.htp[htp_threshold]['htrefs'])
and r.pmid in pmdata and 'pubdate' in pmdata[r.pmid]
]
if len(pms) > 0:
yrs = [int(pmdata[pm]['pubdate'][:4]) for pm in pms]
earliest.append((s, 0, min(yrs), '', e.index))
for pm in pms:
points.append((s, pm, int(pmdata[pm]['pubdate'][:4]),
pmdata[pm]['source'], e.index))
points = common.uniq_list(points)
earliest = common.uniq_list(earliest)
points = pd.DataFrame.from_records(points)
earliest = pd.DataFrame.from_records(earliest)
points.columns = ['database', 'pmid', 'year', 'journal', 'eid']
earliest.columns = ['database', 'none', 'year', 'none', 'eid']
return points, earliest
def write_set(self, id_list, setname, id_type, map_ids=True):
self.sets[setname] = set(common.uniq_list(common.flat_list(
self.mapper.map_name(n, self.ids[id_type], self.target_id)
for n in id_list))) if map_ids \
else set(id_list)
def take_a_trip(cachefile=None):
"""
Downloads TRIP data from webpage and preprocesses it.
Saves preprocessed data into `cachefile` and next
time loads from this file.
:arg cachefile str:
Path to pickle dump of preprocessed TRIP database. If does not exist
the database will be downloaded and saved to this file. By default
the path queried from the ``settings`` module.
"""
cachefile = cachefile or settings.get('trip_preprocessed')
if os.path.exists(cachefile):
_log('Loading preprocessed TRIP database '
'content from `%s`' % cachefile)
result = pickle.load(open(cachefile, 'rb'))
return result
_log('No cache found, downloading and preprocessing TRIP database.')
result = {'sc': {}, 'cc': {}, 'vvc': {}, 'vtc': {}, 'fc': {}}
intrs = {}
titles = {
'Characterization': 'cc',
'Screening': 'sc',
'Validation: In vitro validation': 'vtc',
'Validation: In vivo validation': 'vvc',
'Functional consequence': 'fc',
}
interactors = {}
base_url = urls.urls['trip']['base']
show_url = urls.urls['trip']['show']
c = curl.Curl(base_url)
mainhtml = c.result
mainsoup = bs4.BeautifulSoup(mainhtml, 'html.parser')
trppages = common.flat_list(
[[a.attrs['href'] for a in ul.find_all('a')] for ul in mainsoup.find(
'div', id='trp_selector').find('ul').find_all('ul')])
for trpp in trppages:
trp = trpp.split('/')[-1]
trpurl = show_url % trp
c = curl.Curl(trpurl, silent=False)
trphtml = c.result
trpsoup = bs4.BeautifulSoup(trphtml, 'html.parser')
trp_uniprot = trip_find_uniprot(trpsoup)
if trp_uniprot is None or len(trp_uniprot) < 6:
_log('Could not find UniProt for %s' % trp)
for tab in trpsoup.find_all('th', colspan=['11', '13']):
ttl = titles[tab.text.strip()]
tab = tab.find_parent('table')
trip_process_table(tab, result[ttl], intrs, trp_uniprot)
_log('Saving processed TRIP database content to `%s`' % cachefile)
pickle.dump(result, open(cachefile, 'wb'))
return result
def trip_process(
exclude_methods=['Inference', 'Speculation'],
predictions=False,
species='Human',
strict=False,
):
"""
Downloads TRIP data by calling `pypath.dadio.take_a_trip()` and
further provcesses it.
Returns dict of dict with TRIP data.
@exclude_methods : list
Interaction detection methods to be discarded.
@predictions : bool
Whether to include predicted interactions.
@species : str
Organism name, e.g. `Human`.
@strict : bool
Whether include interactions with species not
used as a bait or not specified.
"""
nd = 'Not determined'
spec = set([]) if strict \
else set(['Not specified', 'Not used as a bait', ''])
spec.add(species)
result = {}
data = take_a_trip()
for uniprots in common.uniq_list(
common.flat_list([v.keys() for v in data.values()])):
to_process = False
refs = set([])
mets = set([])
tiss = set([])
reg = set([])
eff = set([])
if uniprots in data['sc']:
for sc in data['sc'][uniprots]:
if sc[4] in spec and sc[6] in spec and \
(predictions or sc[9] != 'Prediction') and \
sc[3] not in exclude_methods:
refs.add(sc[10])
mets.add(sc[3])
tiss.add(sc[7])
if uniprots in data['vtc']:
for vtc in data['vtc'][uniprots]:
if vtc[4] in spec and vtc[7] in spec and \
vtc[3] not in exclude_methods:
refs.add(vtc[10])
mets.add(vtc[3])
if uniprots in data['vvc']:
for vvc in data['vvc'][uniprots]:
if vvc[6] in spec and vvc[8] in spec and \
vvc[3] not in exclude_methods:
refs.add(vvc[10])
mets.add(vvc[3])
if len(vvc[4]) > 0:
tiss.add(vvc[4])
if len(vvc[5]) > 0:
tiss.add(vvc[5])
if uniprots in data['cc']:
for cc in data['cc'][uniprots]:
if cc[4] in spec and cc[6] in spec and \
cc[3] not in exclude_methods:
refs.add(cc[10])
mets.add(cc[3])
if (cc[5] != nd and len(cc[5]) > 0) or \
(cc[7] != nd and len(cc[7]) > 0):
reg.add((cc[5], cc[7]))
if uniprots in data['fc']:
for fc in data['fc'][uniprots]:
mets.add(fc[3])
refs.add(fc[7])
if len(fc[5]) > 0:
eff.add(fc[5])
if len(fc[6]) > 0:
eff.add(fc[6])
if len(refs) > 0:
result[uniprots] = {
'refs': refs,
'methods': mets,
'tissues': tiss,
'effect': eff,
'regions': reg
}
return result