def report(self, string):
"""Append a string to the report file"""
if not self.report_file:
from hpf.utilities.paths import ensure
ensure(self.job)
self.report_file = open(os.path.join(self.job,"report.txt"), "a")
print >>self.report_file, string
def gather():
util.debug("Gathering result")
job_results = results
paths.ensure(job_results)
#aazj00103_05.075_v1_3.bz2 zj001.fasta zj001.psipred_ss2
#aazj00109_05.075_v1_3.bz2 zj001.psipred
aa_pattern = "aa" + name + "(03|09)\_05\.075\_v1\_3$"
patterns = [aa_pattern]
for suf in [".fasta", ".psipred", ".psipred_ss2"]:
patterns.append(name + suf)
try:
for pattern in patterns:
print "Pattern ", pattern
match = paths.find(pattern, scr_job)
if not match:
raise "Missing file"
for path in match:
if pattern == aa_pattern:
print "Filtering Columns %s" % path
for line in fileinput.input(path, inplace=1):
print " " + line[:47].strip()
fileinput.close()
print "Path ", path
file = paths.getFile(path)
dest = paths.join(job_results, file)
util.copy(path, job_results)
if pattern == aa_pattern:
util.system("bzip2 %s" % dest)
except:
paths.removerf(job_results)
raise
def gather():
util.debug("Gathering result")
job_results = results
paths.ensure(job_results)
#aazj00103_05.075_v1_3.bz2 zj001.fasta zj001.psipred_ss2
#aazj00109_05.075_v1_3.bz2 zj001.psipred
aa_pattern = "aa"+name+"(03|09)\_05\.075\_v1\_3$"
patterns = [aa_pattern]
for suf in [".fasta", ".psipred", ".psipred_ss2"]:
patterns.append(name+suf)
try:
for pattern in patterns:
print "Pattern ",pattern
match = paths.find(pattern, scr_job)
if not match:
raise "Missing file"
for path in match:
if pattern == aa_pattern:
print "Filtering Columns %s" % path
for line in fileinput.input(path, inplace=1):
print " "+line[:47].strip()
fileinput.close()
print "Path ", path
file = paths.getFile(path)
dest = paths.join(job_results, file)
util.copy(path, job_results)
if pattern == aa_pattern:
util.system("bzip2 %s" % dest)
except:
paths.removerf(job_results)
raise
def __enter__(self):
from hpf.utilities.paths import ensure
ensure(self.scratch)
self.session = Session()
runtime().debug("Loading outfile")
self.filesystem_outfile = self.session.query(FilesystemOutfile).filter(FilesystemOutfile.prediction_code==self.prediction_code).first()
runtime().debug("Loading sequence")
self.sequence = self.session.query(Sequence).get(self.filesystem_outfile.sequence_key)
debug(self.prediction_code,self.filesystem_outfile,self.sequence)
return self
def _replicate(self):
"""Copy input files to the job directory ins scratch"""
global scr_job
from hpf.utilities.paths import ensure
ensure(self.job)
self.decoy_file = self._extract(self.decoy_file)
if not self.decoy_file.endswith(".out"):
destination = self.decoy_file+".out"
shutil.move(self.decoy_file, destination)
self.decoy_file = destination
self.psipred_file = self._extract(self.psipred_file)
def gather():
global code, task_id
utilities.debug("Gathering result")
paths.ensure(results_dir)
# Contents of results directory (3' library, 9' library, fasta, psipred, and psipred_ss2 files). EG:
#aazj00103_05.075_v1_3.bz2 zj001.fasta zj001.psipred_ss2
#aazj00109_05.075_v1_3.bz2 zj001.psipred
# Set "patterns" for results files.
aa_pattern = "aa"+code+task_id+"(03|09)\_05\.075\_v1\_3$"
patterns = [aa_pattern]
for suf in [".fasta", ".psipred", ".psipred_ss2"]:
patterns.append(code+task_id+suf)
try:
for pattern in patterns:
print "Pattern ",pattern
# Find the results file in scr_job_dir
match = paths.find(pattern, scr_job_dir)
# If a results file matching pattern is not found in the scr_jobs_dir, raise exception.
if not match:
raise "Missing file"
# Copy all results files in scr_job_dir to results_dir.
for path in match:
# If the results file is a frag library, format the frag library file.
if pattern == aa_pattern:
print "Filtering Columns of file %s" % path
# fileinput.input opens a file for iteration. Defining inplace=1 allows to given file to be
# altered "in place": file is backed up, and stdout is then directed to the file.
# Filters the file: writes " " + first 47 chars of the line. (Specific formatting).
for line in fileinput.input(path, inplace=1):
print " "+line[:47].strip()
fileinput.close()
print "Path ", path
# Copy the result file to results_dir.
utilities.copy(path, results_dir)
# If the results file is a frag library, bzip it in the results_dir.
if pattern == aa_pattern:
dest = paths.join(results_dir, paths.getFile(path))
utilities.system("bzip2 %s" % dest)
# If gathering the results files fails, delete the results_dir and exit.
except:
paths.removerf(results_dir)
raise
def gather():
global code, task_id
utilities.debug("Gathering result")
paths.ensure(results_dir)
# Contents of results directory (3' library, 9' library, fasta, psipred, and psipred_ss2 files). EG:
#aazj00103_05.075_v1_3.bz2 zj001.fasta zj001.psipred_ss2
#aazj00109_05.075_v1_3.bz2 zj001.psipred
# Set "patterns" for results files.
aa_pattern = "aa" + code + task_id + "(03|09)\_05\.075\_v1\_3$"
patterns = [aa_pattern]
for suf in [".fasta", ".psipred", ".psipred_ss2"]:
patterns.append(code + task_id + suf)
try:
for pattern in patterns:
print "Pattern ", pattern
# Find the results file in scr_job_dir
match = paths.find(pattern, scr_job_dir)
# If a results file matching pattern is not found in the scr_jobs_dir, raise exception.
if not match:
raise "Missing file"
# Copy all results files in scr_job_dir to results_dir.
for path in match:
# If the results file is a frag library, format the frag library file.
if pattern == aa_pattern:
print "Filtering Columns of file %s" % path
# fileinput.input opens a file for iteration. Defining inplace=1 allows to given file to be
# altered "in place": file is backed up, and stdout is then directed to the file.
# Filters the file: writes " " + first 47 chars of the line. (Specific formatting).
for line in fileinput.input(path, inplace=1):
print " " + line[:47].strip()
fileinput.close()
print "Path ", path
# Copy the result file to results_dir.
utilities.copy(path, results_dir)
# If the results file is a frag library, bzip it in the results_dir.
if pattern == aa_pattern:
dest = paths.join(results_dir, paths.getFile(path))
utilities.system("bzip2 %s" % dest)
# If gathering the results files fails, delete the results_dir and exit.
except:
paths.removerf(results_dir)
raise
def _gather(self):
"""Gather result files and report text file."""
from hpf.utilities.paths import ensure, find
scr_results_dir = self.decoy_file+".p"
results = os.path.join(self.results,self.job_name)
ensure(results)
# Using the full filename will ensure the directory is created.
shutil.copy(os.path.join(scr_results_dir, "log.xml"), results)
decoys = list(find("decoy\_[0-9]+\.pdb",dir=scr_results_dir))
assert len(decoys)>0
for decoy in decoys:
shutil.copy(decoy, results)
shutil.copy(os.path.join(self.job, "report.txt"), results)
def _dir_setup(self):
# Create results and working directories.
paths.ensure(self.results_dir)
paths.ensure(self.working_dir)
#try:
# os.makedirs(self.results_dir)
# os.makedirs(self.working_dir)
#except OSError as e:
# print e.errno, e.strerror
# raise
# Change directory to working directory.
os.chdir(self.working_dir)
def run(self):
from hpf.utilities.paths import ensure
if self.filesystem_outfile.executable_key==179:
runtime().debug("HPF1 format",self.filesystem_outfile)
_format = self.hpf1
else:
runtime().debug("HPF2 format",self.filesystem_outfile)
_format = self.hpf2
debug("Using decoy format",_format)
self.decoy = format(_format, self.prediction_code)
if not os.path.exists(self.decoy):
debug("NO DECOY FILE",self.prediction_code,self.decoy)
#return None
else:
self.destination = os.path.join(self.scratch,os.path.basename(self.decoy))
if not os.path.exists(self.destination):
ensure(os.path.join(self.scratch,self.prediction_code))
self.decoy = self._decoy()
else:
debug("exists",self.destination)
self.decoy = self.destination
self.psipred = os.path.join(self.scratch,self.prediction_code,self.prediction_code+".psipred")
if not os.path.exists(self.psipred):
ensure(os.path.join(self.scratch,self.prediction_code))
self.psipred = self._ss()
else:
debug("exists",self.psipred)
if all(map(os.path.exists,[self.decoy,self.psipred])):
runtime().debug("Exported",(self.decoy,self.psipred))
return (self.decoy,self.psipred)
else:
runtime().debug("Failed to export")
return None
def replicate():
# Create scr_job_dir
paths.ensure(scr_job_dir)
replicate_fasta()
def replicate():
paths.ensure(scr_job)
replicate_fasta()
def replicate():
paths.ensure(scr_job)
replicate_fasta()
def replicate():
# Create scr_job_dir
paths.ensure(scr_job_dir)
replicate_fasta()
