def replicate_fasta():
if not paths.exists(scr_fasta):
utilities.debug("Replicating fasta file")
utilities.copy(fasta_file, scr_fasta)
paths.existsOrFail(scr_fasta)
def replicate_fasta():
if not paths.exists(scr_fasta):
utilities.debug("Replicating fasta file")
utilities.copy(fasta_file, scr_fasta)
paths.existsOrFail(scr_fasta)
def replicate_fasta():
global scr_fasta
file = paths.getFile(fasta_file)
scr_fasta = paths.join(scr_job, file)
if not paths.exists(scr_fasta):
util.debug("Replicating fasta file")
util.copy(fasta_file, scr_fasta)
paths.existsOrFail(scr_fasta)
def replicate_fasta():
global scr_fasta
file = paths.getFile(fasta_file)
scr_fasta = paths.join(scr_job, file)
if not paths.exists(scr_fasta):
util.debug("Replicating fasta file")
util.copy(fasta_file, scr_fasta)
paths.existsOrFail(scr_fasta)
def _set_env(self):
# Put local variables rep'ing tools and DBs into the environment (via os.environ).
env = {
'BLAST_DIR': self.blast,
'NNMAKE_SHORT_DIR': self.nnmake_short,
'PSIPRED_DIR': self.psipred,
'JUFO_DIR': self.jufo,
'SAM_DIR': self.sam,
'SAM_2ND_DIR': self.sam_2nd,
'NR_DIR': self.nr,
'NNMAKEDB_DIR': self.nnmakedb,
}
for key in env:
# If paths exist, put in Environment (otherwise, fail).
paths.existsOrFail(env[key])
os.environ[key] = env[key]
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)