def setUp(self):
test_input = test_genbank.yeast
self.test_file = "test.gbk"
self.out_file = "out.fa"
handle = open(self.test_file,'w')
handle.write(test_input)
handle.close()
genbank_annotation.parse("NC_12345",self.test_file,open(self.out_file,'w'))
def go(root_dir,output_file,index_obj=None,types=[".gbk",".gff"]):
outHandle = open(output_file,'w')
for root, subFolders, files in os.walk(root_dir):
for fname in files:
genome_files = []
organism,ext = os.path.splitext(os.path.basename(fname))
if ext==".gbk" and ext in types:
absfile=os.path.join(root,fname)
genbank_annotation.parse(organism,absfile,outHandle)
elif ext==".gff" and ext in types:
absfile=os.path.join(root,fname)
gff_annotation.parse(organism,absfile,index_obj,outHandle)
