def runtbl2asn(folder, template, discrepency, organism, isolate, strain,
parameters, version):
'''
function to run NCBI tbl2asn
'''
#get funannotate version
fun_version = lib.get_version()
#input should be a folder
if not os.path.isdir(folder):
log.error("tbl2asn error: %s is not a directory, exiting" % folder)
sys.exit(1)
#based on organism, isolate, strain, construct meta info for -j flag
if not organism:
log.error("tbl2asn error: organism not specified")
sys.exit(1)
meta = "[organism=" + organism + "]"
if isolate:
isolate_meta = "[isolate=" + isolate + "]"
meta = meta + " " + isolate_meta
if strain:
strain_meta = "[strain=" + strain + "]"
meta = meta + " " + strain_meta
cmd = [
'tbl2asn', '-y', '"Annotated using ' + fun_version + '"', '-N',
str(version), '-p', folder, '-t', template, '-M', 'n', '-Z',
discrepency, '-j', '"' + meta + '"', '-V', 'b', '-c', 'fx', '-T', '-a',
'r10u'
]
#check for custom parameters
if parameters:
params = parameters.split(' ')
cmd = cmd + params
runSubprocess(cmd, '.')
return ' '.join(cmd)
#create log file
log_name = os.path.join(args.out, 'logfiles', 'funannotate-train.log')
if os.path.isfile(log_name):
os.remove(log_name)
#initialize script, log system info and cmd issue at runtime
lib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv) + '\n'
lib.log.debug(cmd_args)
print "-------------------------------------------------------"
lib.SystemInfo()
#get version of funannotate
version = lib.get_version()
lib.log.info("Running %s" % version)
#do some checks and balances
if not args.PASAHOME:
try:
PASA = os.environ["PASAHOME"]
except KeyError:
lib.log.error(
"$PASAHOME environmental variable not found, PASA is not properly configured. You can use the --PASAHOME argument to specifiy a path at runtime"
)
sys.exit(1)
else:
PASA = args.PASAHOME
#try to autodetect different PASA distributions
'psutil': '4.0.0',
'natsort': '4.0.0',
'goatools': '0.6.4',
'seaborn': '0.7.0',
'biopython': '1.65'
}
PyVers = sys.version.split(' ')[0]
PerlVers = perlVersion()
PyDeps = {}
PerlDeps = {}
ExtDeps = {}
#loop through lists and build dictionary of results so you can print out later
print("-------------------------------------------------------")
print("Checking dependencies for %s" % lib.get_version())
print("-------------------------------------------------------")
show = False
if len(sys.argv) > 1:
if sys.argv[1] == '--show-versions':
show = True
else:
print(
"To print all dependencies and versions: funannotate check --show-versions\n"
)
print('You are running Python v %s. Now checking python packages...' % PyVers)
for mod in funannotate_python:
if not mod in PyDeps:
PyDeps[mod] = checkPyModule(mod)
#create log file
log_name = os.path.join(args.out, 'funnannotate-compare.log')
if os.path.isfile(log_name):
os.remove(log_name)
#initialize script, log system info and cmd issue at runtime
lib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv)+'\n'
lib.log.debug(cmd_args)
print "-------------------------------------------------------"
lib.SystemInfo()
#get version of funannotate
version = lib.get_version()
lib.log.info("Running %s" % version)
if args.outgroup:
if not os.path.isdir(os.path.join(parentdir, 'DB', 'outgroups')):
lib.log.error("Outgroup folder is not properly configured")
os._exit(1)
files = [f for f in os.listdir(os.path.join(parentdir, 'DB', 'outgroups'))]
files = [ x.replace('_buscos.fa', '') for x in files ]
files = [ x for x in files if not x.startswith('.') ]
if not args.outgroup in files:
lib.log.error("%s is not found in outgroups" % args.outgroup)
print natsorted(files)
else:
outgroup = True
outgroup_species = os.path.join(parentdir, 'DB', 'outgroups', args.outgroup+'_buscos.fa')
