def main():
'''
general gist: loads necessary information, then calls parseLines() which returns a valid sentence to be parsed, valid meaning we are going to throw it in TEES or other NLP program.
'''
args = parseArgs()
logging.info("Parsed arguments")
geneFinder.initData(exclMarkerTypes=["dnaSeq"
]) # setup for findGenes() later
logging.info("Set up environment for findGenes()")
logging.info("Load pickled/marshaled relex, authors, entrez symbols")
relex = pickle.load(args.extractionData)
authors = pickle.load(args.extractionData)
entrez = marshal.load(args.entrezData)['entrez2sym']
logging.info("Open output files")
sentenceFile, geneFile = open(args.timestamp + '-sentence.txt',
'w'), open(args.timestamp + '-genes.txt',
'w')
for pmid, sentence, geneIds, geneNames, rawNames, relations in parseLines(
args.inputFiles, entrez, relex, authors):
geneFile.write(
formatMeta(pmid, geneIds, geneNames, rawNames, relations))
print formatMeta(pmid, geneIds, geneNames, rawNames, relations)
sentenceFile.write(sentence + '\n')
geneFile.flush()
if len(nonamed) > 1:
logging.warning("Not in entrez2sym: {}".format(nonamed))
def main():
'''
general gist: loads necessary information, then calls parseLines() which returns a valid sentence to be parsed, valid meaning we are going to throw it in TEES or other NLP program.
'''
args = parseArgs()
logging.info("Parsed arguments")
geneFinder.initData(exclMarkerTypes=["dnaSeq"]) # setup for findGenes() later
logging.info("Set up environment for findGenes()")
logging.info("Load pickled/marshaled relex, authors, entrez symbols")
relex = pickle.load(args.extractionData)
authors = pickle.load(args.extractionData)
entrez = marshal.load(args.entrezData)['entrez2sym']
logging.info("Open output files")
sentenceFile, geneFile = open(args.timestamp+'-sentence.txt', 'w'), open(args.timestamp+'-genes.txt', 'w')
for pmid, sentence, geneIds, geneNames, rawNames, relations in parseLines(args.inputFiles, entrez, relex, authors):
geneFile.write(formatMeta(pmid, geneIds, geneNames, rawNames, relations))
print formatMeta(pmid, geneIds, geneNames, rawNames, relations)
sentenceFile.write(sentence + '\n')
geneFile.flush()
if len(nonamed) > 1:
logging.warning("Not in entrez2sym: {}".format(nonamed))
def startup(paramDict):
""" parse HUGO file into dict """
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(self, paramDict):
" called once upon startup on each cluster node "
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
self.rowCount = 0
def startup(paramDict):
""" parse HUGO file into dict """
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(paramDict):
varFinder.loadDb()
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(self, paramDict):
" called once upon startup on each cluster node "
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
self.rowCount = 0
def startup(paramDict):
geneFinder.initData(exclMarkerTypes=["dnaSeq", "band"])
#varFinder.loadDb(loadSequences=False)
varFinder.loadDb()
def startup(paramDict):
varFinder.loadDb()
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(self, paramDict, resultDict):
self.maxCount = paramDict["maxCount"]
kwFilename = paramDict["keywords"]
self.searchTypes = getSearchTypes(paramDict)
geneFinder.initData(self.searchTypes, addOptional=True)
def startup(self, paramDict):
""" parse dictioary of keywords """
#self.searchTypes = getSearchTypes(paramDict)
geneFinder.initData(addOptional=True)
def startup(paramDict):
"""
"""
global seqCache
# don't use seqs for gene finding
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(self, paramDict):
""" parse dictioary of keywords """
#self.searchTypes = getSearchTypes(paramDict)
geneFinder.initData(addOptional=True)
def startup(self, paramDict, resultDict):
self.maxCount = paramDict["maxCount"]
kwFilename = paramDict["keywords"]
self.searchTypes = getSearchTypes(paramDict)
geneFinder.initData(self.searchTypes, addOptional=True)
def startup(paramDict):
"""
"""
global seqCache
# don't use seqs for gene finding
geneFinder.initData(exclMarkerTypes=["dnaSeq"])
def startup(paramDict):
geneFinder.initData(exclMarkerTypes=["dnaSeq", "band"])
#varFinder.loadDb(loadSequences=False)
varFinder.loadDb()
