def __processGffFilesNotNew(self, changed):
for gff in changed:
loc = os.path.dirname(gff)
dbName = os.path.splitext(os.path.basename(gff))[0] + '.db'
dbName = os.path.join(loc, dbName)
gffRewriter = GFFRewriter(filename=gff,
outfile=gff + ".sorted.prepared",
accession=genbank_id)
#print setting.DATABASES['default']['USER']
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':
'go'
})
error = gffRewriter.getError()
# run the sqlite database loader to be able to add it to GBrowse
# since the name should be preserved, no changes need to be made
# to the GBrowse configuration file
args = ['-a', 'DBI::SQLite', '-c', '-f', '-d', dbName, gff]
runProgram('bp_seqfeature_load.pl', args)
parser = GenBank.RecordParser()
gbk = os.path.join(os.path.splitext(gff)[0], '.gbk')
record = parser.parse(open(gbk))
organismName = record.organism
organismDir = os.path.basename(loc)
GenomeDBUtil.editGBrowseEntry(gff, dbName, organismDir,
organismName)
# now edit the record in Chado
args = [
'--organism', organismName, "--gfffile", gff, "--dbname",
settings.DATABASES['default']['NAME'], "--dbuser",
settings.DATABASES['default']['USER'], "--dbpass",
settings.DATABASES['default']['PASSWORD'], "--random_tmp_dir"
]
runProgram('gmod_bulk_load_gff3.pl', args)
def __processGffFilesNotNew(self, changed):
for gff in changed:
loc = os.path.dirname(gff)
dbName = os.path.splitext(os.path.basename(gff))[0] + '.db'
dbName = os.path.join(loc, dbName)
gffRewriter = GFFRewriter(filename=gff, outfile=gff+".sorted.prepared" , accession=genbank_id)
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()
# run the sqlite database loader to be able to add it to GBrowse
# since the name should be preserved, no changes need to be made
# to the GBrowse configuration file
args = ['-a', 'DBI::SQLite', '-c', '-f', '-d', dbName, gff]
runProgram('bp_seqfeature_load.pl', args)
parser = GenBank.RecordParser()
gbk = os.path.join(os.path.splitext(gff)[0], '.gbk')
record = parser.parse(open(gbk))
organismName = record.organism
organismDir = os.path.basename(loc)
GenomeDBUtil.editGBrowseEntry(gff, dbName, organismDir, organismName)
# now edit the record in Chado
args= ['--organism', organismName, "--gfffile", gff, "--dbname", settings.DATABASES['default']['NAME'], "--dbuser", settings.DATABASES['default']['USER'], "--dbpass", settings.DATABASES['default']['PASSWORD'], "--random_tmp_dir"]
runProgram('gmod_bulk_load_gff3.pl', args)
