if not os.path.isdir(os.path.join(outputdir, 'annotate_misc')):
os.makedirs(os.path.join(outputdir, 'annotate_misc'))
if not os.path.isdir(os.path.join(outputdir, 'annotate_results')):
os.makedirs(os.path.join(outputdir, 'annotate_results'))
if not os.path.isdir(os.path.join(outputdir, 'logfiles')):
os.makedirs(os.path.join(outputdir, 'logfiles'))
genbank = args.genbank
Scaffolds = os.path.join(outputdir, 'annotate_misc',
'genome.scaffolds.fasta')
Proteins = os.path.join(outputdir, 'annotate_misc',
'genome.proteins.fasta')
Transcripts = os.path.join(outputdir, 'annotate_misc',
'genome.transcripts.fasta')
GFF = os.path.join(outputdir, 'annotate_misc', 'genome.gff3')
lib.log.info("Checking GenBank file for annotation")
if not lib.checkGenBank(genbank):
lib.log.error("Found no annotation in GenBank file, exiting")
sys.exit(1)
lib.gb2allout(genbank, GFF, Proteins, Transcripts, Scaffolds)
else:
#should be a folder, with funannotate files, thus store results there, no need to create output folder
if not os.path.isdir(args.input):
lib.log.error("%s directory does not exist" % args.input)
sys.exit(1)
if os.path.isdir(os.path.join(
args.input,
'update_results')): #funannotate results should be here
inputdir = os.path.join(args.input, 'update_results')
outputdir = args.input
elif os.path.isdir(os.path.join(args.input, 'predict_results')):
os.makedirs(outputdir)
os.makedirs(os.path.join(outputdir, 'annotate_misc'))
os.makedirs(os.path.join(outputdir, 'annotate_results'))
else:
lib.log.error("Output directory %s already exists, will use any existing data. If this is not what you want, exit, and provide a unique name for output folder" % (outputdir))
if not os.path.isdir(os.path.join(outputdir, 'annotate_misc')):
os.makedirs(os.path.join(outputdir, 'annotate_misc'))
if not os.path.isdir(os.path.join(outputdir, 'annotate_results')):
os.makedirs(os.path.join(outputdir, 'annotate_results'))
genbank = args.genbank
Scaffolds = os.path.join(outputdir, 'annotate_misc', 'genome.scaffolds.fasta')
Proteins = os.path.join(outputdir, 'annotate_misc', 'genome.proteins.fasta')
Transcripts = os.path.join(outputdir, 'annotate_misc', 'genome.transcripts.fasta')
GFF = os.path.join(outputdir, 'annotate_misc', 'genome.gff3')
lib.log.info("Checking GenBank file for annotation")
if not lib.checkGenBank(genbank):
lib.log.error("Found no annotation in GenBank file, exiting")
os._exit(1)
lib.gb2allout(genbank, GFF, Proteins, Transcripts, Scaffolds)
else:
#should be a folder, with funannotate files, thus store results there, no need to create output folder
if not os.path.isdir(args.input):
lib.log.error("%i directory does not exist" % args.input)
os._exit(1)
if os.path.isdir(os.path.join(args.input, 'predict_results')): #funannotate results should be here
inputdir = os.path.join(args.input, 'predict_results')
outputdir = args.input
else:
inputdir = os.path.join(args.input) #here user specified the predict_results folder, or it is all together wrong, find out in next few lines
#get files that you need