def __processGffFilesNew(self, newOrganismDirs):
for newOrganism in newOrganismDirs:
# start by creating the BLAST database
newOrganism = os.path.join(NEW_GENOMIC_DATA_DIR, newOrganism)
print newOrganism
organismFiles = os.walk(newOrganism).next()[2]
faa = None
ffn = None
gff = None
gbk = None
for organismFile in organismFiles:
extension = os.path.splitext(organismFile)[1]
if (extension == '.ffn'):
ffn = organismFile
elif (extension == '.faa'):
faa = organismFile
elif (extension == '.gff'):
gff = organismFile
elif (extension == '.gbk'):
gbk = organismFile
if (faa and ffn and gff and gbk):
break
if (faa):
GenomeDBUtil.runFormatDB(os.path.basename(faa), newOrganism, protein=True)
self.report.addLogEntry('Ran formatdb successully on ' + faa)
if (ffn):
GenomeDBUtil.runFormatDB(os.path.basename(ffn), newOrganism, protein=False)
self.report.addLogEntry('Ran formatdb successully on ' + ffn)
# process the gff and genbank files for creating the databases
if (gff and gbk):
# create the sqlite database for GBrowse and create the configuration file
# for GBrowse hook up
dbName = os.path.splitext(os.path.basename(gff))[0] + '.db'
dbName = os.path.join(newOrganism, dbName)
gff = os.path.join(newOrganism, gff)
parser = GenBank.RecordParser()
gbk = os.path.join(newOrganism, gbk)
record = parser.parse(open(gbk))
organismName = record.organism
accession = record.accession[0]
self.report.addLogEntry('Found organism name ' + organismName)
# create a brand new GBrowse configuration file
examiner = GFFExaminer()
gffHandle = open(gff)
landmark = examiner.available_limits(gffHandle)['gff_id'].keys()[0][0]
gffRewriter = GFFRewriter(filename=gff, outfile=gff+".sorted.prepared" , accession=accession)
'''gffRewriter.addUnknownCvTerms({
'user' : settings.DATABASES['default']['USER'],
'password' : settings.DATABASES['default']['PASSWORD'],
'db' : settings.DATABASES['default']['NAME']
})'''
gffRewriter.addColor({
'user' : settings.DATABASES['default']['USER'],
'password' : settings.DATABASES['default']['PASSWORD'],
'db' : 'MyGO'
})
error = gffRewriter.getError()
print error
gff = gff + ".sorted.prepared"
args = ['-a', 'DBI::SQLite', '-c', '-f', '-d', dbName, gff]
runProgram('bp_seqfeature_load.pl', args)
self.report.addLogEntry('Successfully created sqlite database for ' + str(gff))
organismDir = os.path.basename(newOrganism)
self.report.addLogEntry('Added new GBrowse entry for ' + organismName)
# now edit the record in Chado by first adding the organism and then adding
# bulk loading the information from gff3
id = GenomeDBUtil.addOrganismToChado(gff, organismName)
GenomeDBUtil.createNewGBrowseEntry(landmark, dbName, organismDir, organismName, id)
