args.input
) #here user specified the predict_results folder, or it is a custom folder
#get files that you need
for file in os.listdir(inputdir):
if file.endswith('.gbk'):
genbank = os.path.join(inputdir, file)
#now create the files from genbank input file for consistency in gene naming, etc
if not genbank:
lib.log.error(
"Properly formatted 'funannotate predict' files do no exist in this directory"
)
sys.exit(1)
else:
if 'predict_results' in inputdir or 'update_results' in inputdir: #if user gave predict_results folder, then set output to up one directory
outputdir = lib.get_parent_dir(inputdir)
else:
if not args.out:
outputdir = inputdir #output the results in the input directory
else:
outputdir = args.out
if not os.path.isdir(outputdir):
os.makedirs(outputdir)
#create output directories
if not os.path.isdir(os.path.join(outputdir, 'annotate_misc')):
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))
lib.CheckDependencies(programs)
#take care of some preliminary checks
SBT = args.sbt
#need to do some checks here of the input
#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
outputdir = lib.get_parent_dir(args.input)
#get files that you need
for file in os.listdir(inputdir):
if file.endswith('.scaffolds.fa'):
Scaffolds = os.path.join(inputdir, file)
if file.endswith('.gff3'):
GFF = os.path.join(inputdir, file)
#now get the AGP file - this will be in annotate_results folder
if os.path.isdir(os.path.join(outputdir, 'annotate_results')):
for file in os.listdir(os.path.join(outputdir, 'annotate_results')):
if file.endswith('.agp'):
AGP = os.path.join(outputdir, 'annotate_results', file)
if file.endswith('.gbk'):
GBK = os.path.join(outputdir, 'annotate_results', file)
if not os.path.isdir(args.input[i]):
if args.input[i].endswith('.gbk') or args.input[i].endswith('.gbff'):
GBK = args.input[i]
else:
lib.log.error(
"Error, %s is not a funannotate folder and does not seem to be a GenBank file."
% args.input[i])
os._exit(1)
else: #split arguments into genomes and run a bunch of stats/comparisons
#look for annotate_results folder
GBK = ''
fun_dir = args.input[i]
if not os.path.isdir(os.path.join(args.input[i], 'annotate_results')
): #this means was not passed the whole folder
fun_dir = lib.get_parent_dir(
args.input[i]
) #set fun_dir up a directory to find other results if needed
for file in os.listdir(args.input[i]):
if file.endswith('.gbk'):
GBK = os.path.join(args.input[i], file)
else: #whole folder is passed, now get the genbank file
for file in os.listdir(
os.path.join(args.input[i], 'annotate_results')):
if file.endswith('.gbk'):
GBK = os.path.join(args.input[i], 'annotate_results', file)
if not GBK: #check this
lib.log.error(
"Error, was not able to find appropriate GenBank file in the annotate_results folder"
)
gbkfilenames.append(GBK)
#now run genome routines
num_input = len(args.input)
if num_input == 0:
lib.log.error("Error, you did not specify an input, -i")
os._exit(1)
lib.log.info("Now parsing %i genomes" % num_input)
for i in range(0,num_input):
#parse the input, I want user to give output folder for funannotate, put they might give a results folder, so do the best you can to check
if not os.path.isdir(args.input[i]):
lib.log.error("Error, one of the inputs is not a folder")
os._exit(1)
else: #split arguments into genomes and run a bunch of stats/comparisons
#look for annotate_results folder
GBK = ''
fun_dir = args.input[i]
if not os.path.isdir(os.path.join(args.input[i], 'annotate_results')): #this means was not passed the whole folder
fun_dir = lib.get_parent_dir(args.input[i]) #set fun_dir up a directory to find other results if needed
for file in os.listdir(args.input[i]):
if file.endswith('.gbk'):
GBK = os.path.join(args.input[i], file)
else: #whole folder is passed, now get the genbank file
for file in os.listdir(os.path.join(args.input[i], 'annotate_results')):
if file.endswith('.gbk'):
GBK = os.path.join(args.input[i], 'annotate_results', file)
if not GBK: #check this
lib.log.error("Error, was not able to find appropriate GenBank file in the annotate_results folder")
gbkfilenames.append(GBK)
#now run genome routines
stats.append(lib.genomeStats(GBK))
merops.append(lib.getStatsfromNote(GBK, 'MEROPS'))
ipr.append(lib.getStatsfromDbxref(GBK, 'InterPro'))
pfam.append(lib.getStatsfromDbxref(GBK, 'PFAM'))
lib.CheckDependencies(programs)
#take care of some preliminary checks
SBT = args.sbt
#need to do some checks here of the input
#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
outputdir = lib.get_parent_dir(args.input)
#get files that you need
for file in os.listdir(inputdir):
if file.endswith('.scaffolds.fa'):
Scaffolds = os.path.join(inputdir, file)
if file.endswith('.gff3'):
GFF = os.path.join(inputdir, file)
#now get the AGP file - this will be in annotate_results folder
if os.path.isdir(os.path.join(outputdir, 'annotate_results')):
for file in os.listdir(os.path.join(outputdir, 'annotate_results')):
if file.endswith('.agp'):
AGP = os.path.join(outputdir, 'annotate_results', file)
if file.endswith('.gbk'):
GBK = os.path.join(outputdir, 'annotate_results', file)
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
for file in os.listdir(inputdir):
if file.endswith('.gbk'):
genbank = os.path.join(inputdir, file)
if file.endswith('.gff3'):
GFF = os.path.join(inputdir, file)
#now create the files from genbank input file for consistency in gene naming, etc
if not genbank or not GFF:
lib.log.error("Properly formatted 'funannotate predict' files do no exist in this directory")
os._exit(1)
else:
if inputdir == outputdir: #I'm assuming means that user supplied the predict folder (probably bad to assume...)
outputdir = lib.get_parent_dir(inputdir)
#create output directories
if not os.path.isdir(os.path.join(outputdir, 'annotate_misc')):
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))
lib.log.info("Parsing input files")
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')
lib.gb2output(genbank, Proteins, Transcripts, Scaffolds)
#get absolute path for all input so there are no problems later
for i in Scaffolds, Proteins, Transcripts, GFF:
i = os.path.abspath(i)