#create log file
log_name = args.logfile
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)
#create tmpdir to store fasta files and output files
TMPDIR = 'phobius_' + str(os.getpid())
#split fasta
lib.splitFASTA(args.input, TMPDIR)
#now get list of files in tmpdir
proteins = []
for file in os.listdir(TMPDIR):
if file.endswith('.fa'):
proteins.append(file)
#now run the script
if lib.which('phobius.pl'):
lib.runMultiProgress(runPhobiusLocal, proteins, multiprocessing.cpu_count())
else:
lib.runMultiProgress(runPhobiusRemote, proteins, 29) #max is 30 jobs at a time
#collect all results
phobius = []
subprocess.call([
os.path.join(parentdir, 'util', 'phobius-multiproc.py'), '-i',
Proteins, '-o', phobius_out, '-l', phobiusLog
])
if 'interproscan' in args.methods or 'all' in args.methods:
IPRCombined = os.path.join(outputdir, 'annotate_misc', 'iprscan.xml')
#run interpro scan
IPROUT = os.path.join(outputdir, 'annotate_misc', 'iprscan')
PROTS = os.path.join(outputdir, 'annotate_misc', 'protein_tmp')
for i in IPROUT, PROTS:
if not os.path.exists(i):
os.makedirs(i)
#now run interproscan
#split input into individual files
lib.splitFASTA(Proteins, PROTS)
#now iterate over list using pool and up to 25 submissions at a time
proteins = []
for file in os.listdir(PROTS):
if file.endswith('.fa'):
file = os.path.join(PROTS, file)
proteins.append(file)
num_files = len(glob.glob1(IPROUT, "*.xml"))
num_prots = len(proteins)
lib.log.info(
"Now running InterProScan search remotely using EBI servers on " +
'{0:,}'.format(num_prots) + ' proteins')
#build in a check before running (in case script gets stopped and needs to restart
finished = []
for file in os.listdir(IPROUT):
num_annotations = lib.line_count(signalp_out)
lib.log.info('{0:,}'.format(num_annotations) + ' annotations added')
else:
lib.log.info("SignalP not installed, skipping")
if not args.skip_iprscan:
if not args.iprscan:
#run interpro scan
IPROUT = os.path.join(outputdir, 'annotate_misc', 'iprscan')
PROTS = os.path.join(outputdir, 'annotate_misc', 'protein_tmp')
for i in IPROUT,PROTS:
if not os.path.exists(i):
os.makedirs(i)
#now run interproscan
#split input into individual files
lib.splitFASTA(Proteins, PROTS)
#now iterate over list using pool and up to 25 submissions at a time
proteins = []
for file in os.listdir(PROTS):
if file.endswith('.fa'):
file = os.path.join(PROTS, file)
proteins.append(file)
num_files = len(glob.glob1(IPROUT,"*.xml"))
num_prots = len(proteins)
lib.log.info("Now running InterProScan search remotely using EBI servers on " + '{0:,}'.format(num_prots) + ' proteins')
while (num_files < num_prots):
#build in a check before running (in case script gets stopped and needs to restart
finished = []
for file in os.listdir(IPROUT):
