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for peptide in proteinEntry.sharedPeptides:
startPos, endPos = peptidedb[peptide].proteinPositions[proteinId]
coverageMaskShared[startPos-1:endPos] = True
setattr(proteinEntry, 'coverageMaskUnique', coverageMaskUnique)
setattr(proteinEntry, 'coverageMaskShared', coverageMaskShared)"
1986,"def fetch_keywords(codedata) :
"""""" Fetch keywords by shaman.KeywordFetcher
Get average probabilities of keyword and language
""""""
# Read row in codedata and count keywords in codes with langauge
tmp = {}
language_counts = {}
for index, (language, code) in enumerate(codedata) :
if language not in shaman.SUPPORTING_LANGUAGES :
continue
if language not in tmp :
tmp[language] = {}
language_counts[language] = 0
language_counts[language] += 1
for keyword in shaman.KeywordFetcher.fetch( code ) :
# if keyword exists in fetched data, add '1' to keyword data
tmp[language][keyword] = tmp[language].get(keyword, 0) + 1
print('Fetch keyword %d/%d ' % (index, len(codedata)), end='\r')
# Get dataset indexed by keyword
ret = {}
for language in tmp :
for keyword, count in tmp[ language ].items() :
if keyword not in ret :
ret[ keyword ] = {}
ret[ keyword ][ language ] = (count / language_counts[ language ]) # Probability
print('Fetch keyword completed ')
return ret"
1987,"def match_patterns(codedata) :
"""""" Match patterns by shaman.PatternMatcher
Get average ratio of pattern and language
""""""
ret = {}
for index1, pattern in enumerate(shaman.PatternMatcher.PATTERNS) :
print('Matching pattern %d ""%s""' % (index1+1, pattern))
matcher = shaman.PatternMatcher(pattern)
tmp = {}
for index2, (language, code) in enumerate(codedata) :
if language not in shaman.SUPPORTING_LANGUAGES :
continue
if len(code) <= 20 or len(code) > 100000 :
continue
if language not in tmp :
tmp[language] = []
ratio = matcher.getratio(code)
tmp[language].append(ratio)
print('Matching patterns %d/%d ' % (index2, len(codedata)), end='\r')
ret[pattern] = {}
for language, data in tmp.items() :
ret[pattern][language] = sum(tmp[language]) / max(len(tmp[language]), 1)
print('Matching patterns completed ')
return ret"
1988,"def facility(self, column=None, value=None, **kwargs):
""""""
Check information related to Radiation facilities.
>>> RADInfo().facility('state_code', 'CA')
""""""
return self._resolve_call('RAD_FACILITY', column, value, **kwargs)"
1989,"def facility_type(self, column=None, value=None, **kwargs):
""""""
Basic identifying information for a RADInfo facility, including
the improved facility information maintained by the Facility
Registry System (FRS).
>>> RADInfo().facility_type('cit_ref_code', '40CFR300')
""""""
return self._resolve_call('RAD_FACILITY_TYPE', column, value, **kwargs)"
1990,"def geo(self, column=None, value=None, **kwargs):
""""""
Locate a facility through geographic location.
>>> RADInfo().geo('geometric_type_code', '001')
""""""