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$"
patterns = [aa_pattern]
for suf in [".fasta", ".psipred", ".psipred_ss2"]:
patterns.append(name+suf)
try:
for pattern in patterns:
print "Pattern ",pattern
match = paths.find(pattern, scr_job)
if not match:
raise "Missing file"
for path in match:
if pattern == aa_pattern:
print "Filtering Columns %s" % path
for line in fileinput.input(path, inplace=1):
print " "+line[:47].strip()
fileinput.close()
print "Path ", path
file = paths.getFile(path)
dest = paths.join(job_results, file)
util.copy(path, job_results)
if pattern == aa_pattern:
util.system("bzip2 %s" % dest)
except:
paths.removerf(job_results)
raise
def _filter_fraglibs(self):
# Runs on fragment picking result 3' and 9' fragment libraries (must exist from Frag run).
# Filters the file inplace: writes " " + first 47 chars of the line. (IBM formatting).
# Also uses bzip2 binary to compress fragment library files (IBM formatting). Can do with bz2 library.
if self.frag3_lib == None or self.frag9_lib == None:
raise Exception("Fragment library results files do not yet exist. Run Fragmentor.run(...) first.")
frag_libs = [self.frag3_lib, self.frag9_lib]
for frag_lib in frag_libs:
# Filter frag library columns.
for line in fileinput.input(frag_lib, inplace=1):
print " "+line[:47].strip()
fileinput.close()
# Bzip frag library file and reset instance variable to reflect new name.
cmd = "bzip2 {0}".format(frag_lib)
system(cmd)
# Update instance variable values to reflect bzip on fragment files.
self.results_files.remove(self.frag3_lib)
self.results_files.remove(self.frag9_lib)
self.frag3_lib = self.frag3_lib+".bz2"
self.frag9_lib = self.frag9_lib+".bz2"
self.results_files.append(self.frag3_lib)
self.results_files.append(self.frag9_lib)
def gather():
util.debug("Gathering result")
job_results = results
paths.ensure(job_results)
#aazj00103_05.075_v1_3.bz2 zj001.fasta zj001.psipred_ss2
#aazj00109_05.075_v1_3.bz2 zj001.psipred
aa_pattern = "aa" + name + "(03|09)\_05\.075\_v1\_3$"
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():
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 run_blast(query_file):
if not isfile(query_file):
raise Exception("Given blast query file {0} not a valid file".format(query_file))
blast_outfile = query_file + '.blast.xml'
blast_cmd = "{0} -i {1} -d {2} -e {3} -v {4} -b {5} -a {6} -m {7} -o {8}".format( \
blast_exe, query_file, source_db, e_val, results, alignments, processors, output_mode, blast_outfile)
print "Blast command: {0}".format(blast_cmd)
try:
system(blast_cmd)
except Exception as e:
print e
print "Blasting query file {0} against DB {1} failed".format(query_file, source_db)
raise
def run_blast(query_file):
if not isfile(query_file):
raise Exception(
"Given blast query file {0} not a valid file".format(query_file))
blast_outfile = query_file + '.blast.xml'
blast_cmd = "{0} -i {1} -d {2} -e {3} -v {4} -b {5} -a {6} -m {7} -o {8}".format( \
blast_exe, query_file, source_db, e_val, results, alignments, processors, output_mode, blast_outfile)
print "Blast command: {0}".format(blast_cmd)
try:
system(blast_cmd)
except Exception as e:
print e
print "Blasting query file {0} against DB {1} failed".format(
query_file, source_db)
raise
def _run_frag(self, nohoms, fasta):
# Takes a boolean nohoms (to pass to script) and the fasta input (filename).
# Check to see if script given in config file exists.
if not os.path.isfile(self.frag_script):
raise Exception("Fragment picking {0} script specified in config file ({1}) is not" \
"accessible.".format(self.frag_script, cofig_file))
# Run the given script on fasta file. Current options: ?-nohoms -nosam -verbose.
if nohoms:
cmd = "{0} -nohoms -nosam -verbose {1}".format(self.frag_script, fasta)
else:
cmd = "{0} -nosam -verbose {1}".format(self.frag_script, fasta)
print "Fragmentor: executing frag command {0}".format(cmd)
system(cmd)
def runScript(no_homs=False):
# Script requires the following environment variables
# BLAST_DIR
# NR_DIR
# NNMAKE_DIR - the BLOSUM score matrices
# PSIPRED_DIR
# NNMAKE_DIR
# JUFO_DIR
# SAM_DIR
# SAM_2ND_DIR - SAM Secondary Structure Prediction
utilities.debug("Running fragmentation script")
env = {
'BLAST_DIR':'%s/blast' % tools_dir,
'NR_DIR':'%s/db/nr' % scr_dir,
'NNMAKEDB_DIR':'%s/db/nnmake_database' % scr_dir,
'NNMAKE_SHORT_DIR':'%s/nnmake' % tools_dir,
'PSIPRED_DIR':'%s/psipred' % tools_dir,
'JUFO_DIR':'%s/jufo' % tools_dir,
'SAM_DIR':'%s/sam' % tools_dir,
'SAM_2ND_DIR':'%s/sam.predict-2nd' % tools_dir
}
for key in env :
# Check if all paths given in env exist.
paths.existsOrFail(env[key])
# os.environ is the system environment. New env. vars. can be set by adding to it.
os.environ[key] = env[key]
script = paths.join(home, "scripts", frag_script)
if no_homs:
script = "%s -nohoms" % script
fasta = paths.getFile(fasta_file)
cmd = "cd %s && %s -verbose -nosam %s" % (scr_job_dir, script, fasta)
#cmd = "cd %s && %s -verbose %s" % (scr_job_dir, script, fasta)
utilities.system(cmd)
def runScript(no_homs=False):
# Script requires the following environment variables
# BLAST_DIR
# NR_DIR
# NNMAKE_DIR - the BLOSUM score matrices
# PSIPRED_DIR
# NNMAKE_DIR
# JUFO_DIR
# SAM_DIR
# SAM_2ND_DIR - SAM Secondary Structure Prediction
utilities.debug("Running fragmentation script")
env = {
'BLAST_DIR': '%s/blast' % tools_dir,
'NR_DIR': '%s/db/nr' % scr_dir,
'NNMAKEDB_DIR': '%s/db/nnmake_database' % scr_dir,
'NNMAKE_SHORT_DIR': '%s/nnmake' % tools_dir,
'PSIPRED_DIR': '%s/psipred' % tools_dir,
'JUFO_DIR': '%s/jufo' % tools_dir,
'SAM_DIR': '%s/sam' % tools_dir,
'SAM_2ND_DIR': '%s/sam.predict-2nd' % tools_dir
}
for key in env:
# Check if all paths given in env exist.
paths.existsOrFail(env[key])
# os.environ is the system environment. New env. vars. can be set by adding to it.
os.environ[key] = env[key]
script = paths.join(home, "scripts", frag_script)
if no_homs:
script = "%s -nohoms" % script
fasta = paths.getFile(fasta_file)
cmd = "cd %s && %s -verbose -nosam %s" % (scr_job_dir, script, fasta)
#cmd = "cd %s && %s -verbose %s" % (scr_job_dir, script, fasta)
utilities.system(cmd)
def runScript():
# Script requires the following environment variables
# BLAST_DIR
# NR_DIR
# NNMAKE_DIR - the BLOSUM score matrices
# PSIPRED_DIR
# NNMAKE_DIR
# JUFO_DIR
# SAM_DIR
# SAM_2ND_DIR - SAM Secondary Structure Prediction
util.debug("Running fragmentation script")
env = {
'BLAST_DIR':'%s/blast' % shareware,
'NR_DIR':'%s/db/nr' % scr,
'NNMAKEDB_DIR':'%s/db/nnmake_database' % scr,
'NNMAKE_SHORT_DIR':'%s/nnmake' % shareware,
'PSIPRED_DIR':'%s/psipred' % shareware,
'JUFO_DIR':'%s/jufo' % shareware,
'SAM_DIR':'%s/sam' % shareware,
'SAM_2ND_DIR':'%s/sam.predict-2nd' % shareware
}
for key in env :
# Make sure all paths in 'env' exist in the system.
paths.existsOrFail(env[key])
# Put 'env' values into the system environment.
os.environ[key] = env[key]
script = paths.join(home, "scripts", pl_script)
if no_homs:
script = "%s -nohoms" % script
fasta = paths.getFile(scr_fasta)
cmd = "cd %s && %s -verbose -nosam %s" % (scr_job, script, fasta)
#cmd = "cd %s && %s -verbose %s" % (scr_job, script, fasta)
util.system(cmd)
def runScript():
# Script requires the following environment variables
# BLAST_DIR
# NR_DIR
# NNMAKE_DIR - the BLOSUM score matrices
# PSIPRED_DIR
# NNMAKE_DIR
# JUFO_DIR
# SAM_DIR
# SAM_2ND_DIR - SAM Secondary Structure Prediction
util.debug("Running fragmentation script")
env = {
'BLAST_DIR': '%s/blast' % shareware,
'NR_DIR': '%s/db/nr' % scr,
'NNMAKEDB_DIR': '%s/db/nnmake_database' % scr,
'NNMAKE_SHORT_DIR': '%s/nnmake' % shareware,
'PSIPRED_DIR': '%s/psipred' % shareware,
'JUFO_DIR': '%s/jufo' % shareware,
'SAM_DIR': '%s/sam' % shareware,
'SAM_2ND_DIR': '%s/sam.predict-2nd' % shareware
}
for key in env:
# Make sure all paths in 'env' exist in the system.
paths.existsOrFail(env[key])
# Put 'env' values into the system environment.
os.environ[key] = env[key]
script = paths.join(home, "scripts", pl_script)
if no_homs:
script = "%s -nohoms" % script
fasta = paths.getFile(scr_fasta)
cmd = "cd %s && %s -verbose -nosam %s" % (scr_job, script, fasta)
#cmd = "cd %s && %s -verbose %s" % (scr_job, script, fasta)
util.system(cmd)
def removerf(path):
from hpf.utilities import system
system("rm -rf %s" % path)
