def gmes(self, fasta):
"""
predict proteins using gmes
"""
logging.debug("Starting gmes function")
gmesDir = os.path.join(self.cfg["outdir"], "workfiles", "gmes")
file.isdir(gmesDir)
gmesOut = os.path.join(gmesDir, "prot_seq.faa")
gtffile = os.path.join(gmesDir, "genemark.gtf")
inputfasta = os.path.abspath(os.path.join(gmesDir, "input.fna"))
# GeneMark-ES
g = gmes("runGMES", fasta, [gtffile, gmesOut], touch=self.cfg["touch"])
logging.debug("Defined gmes run")
if g.doIneedTorun(self.cfg["force"]):
# rename fasta entries, so we dont have white spaces in them
# can be turned of via cleanfasta in config file
if not self.cfg["touch"]:
g.input = base.clearFastaNames(fasta, inputfasta)
else:
g.input = inputfasta
logging.info("Running GeneMark-ES")
g.run(cores=self.cfg["ncores"])
else:
logging.debug("I do not need to run gmes, output exists:")
logging.debug(gtffile)
# always check if gtffile exists, if not Genemark-ES failed and
# we can stop here
if not file.exists(gtffile):
# log and document failing
# then stop pipeline
logging.error("GeneMark-ES failed on this bin")
self.write_outfile()
exit(1)
elif self.cfg["clean"]:
# clean temp dirs
_tmpdirs = ["data", "run", "info", "output/data", "output/gmhmm"]
tempdirs = [os.path.join(gmesDir, x) for x in _tmpdirs]
g.cleanup(tempdirs)
# make a bed file from GTF
bedf = os.path.join(gmesDir, "proteins.bed")
if self.cfg["force"] or file.isnewer(gtffile,
bedf) and not self.cfg["touch"]:
logging.info("Extracting protein locations")
bedf = base.gmesBED(gtffile, bedf)
# touch files expected for next step
if self.cfg["touch"]:
g.touch([bedf, gmesOut])
self._clean_fasta = inputfasta
return (gmesOut, bedf)
def concatHMM(self):
# create a dir for this
hmmdir = os.path.join(self.cfg["outdir"], "workfiles", "hmmer", "estimations")
file.isdir(hmmdir)
hmmconcat = os.path.join(hmmdir, "all.hmm")
if self.cfg["touch"]:
file.touch(hmmconcat)
return hmmconcat
profiles = set()
for p in self.placements[self.cfg["placementMethod"]]:
localpath = os.path.join(self.cfg["db"], "sets", "{}.set".format(p["node"]))
with open(localpath) as f:
for line in f:
profiles.add(line.strip())
# make profiles to sorted list
profiles = list(profiles)
profiles.sort()
# create all paths for all hmms
hmmerpaths = [os.path.join(self.cfg["db"], "hmms", "panther", "{}.hmm".format(profile)) for profile in profiles]
# sort and check if we already have the hmm for this
canuseprev = False
profilehash = hashlib.sha256("_".join(profiles).encode()).hexdigest()
hashpath = os.path.join(hmmdir, "all.hash")
if file.exists(hashpath):
with open(hashpath) as f:
for line in f:
prevhash = line.strip()
break
canuseprev = prevhash == profilehash
if canuseprev:
# we can use the existing file, so no need to continue
log("Using pressed hmms from last run")
return hmmconcat
# concatenate
if len(profiles) == 0:
logging.error("We have no profiles to evaluate")
exit(1)
log("{} hmm profiles need to be used for estimations".format(len(profiles)))
log("Concatenating hmms, this might take a while (IO limited)")
hmmconcat = base.concatenate(hmmconcat, hmmerpaths)
# press
log("Pressing hmms")
hp = hmmpress("hmmpress", hmmconcat, None, touch=self.cfg["touch"])
hp.run()
# save profile hash
with open(hashpath, "w") as f:
f.write(f"{profilehash}")
return hmmconcat