def run(self, input_file, run_locally=True) :
print input_file
bname = splitext( basename(input_file) )[0]
output_dir = "%s/%s/output" % (globes.INT_DIR, self.name)
print output_dir
output_file = "%s/%s.csv" \
% (output_dir, bname)
if not run_locally :
commands = ['cd /projects/gleeson-lab/bin/snpEff_v1_9_5',
'java -Xmx20g -jar snpEff.jar -f hg37 %s' \
% input_file,
'mv %s/output/%s_out.txt %s' \
% (globes.BATCH_DIR,self.name,output_file) ]
batchJob = batch.writeBatchFile('snpeff', commands )
batchJob.submit()
else :
commands = ['cd %s/bin/snpEff_v2_0_2' % (globes.ROOT_DIR), \
'java -Xmx5g -jar snpEff.jar hg37 %s' \
% input_file] #,
filename = "run_snpeff.sh"
shellfile = open(filename, 'wb')
shellfile.write( '\n'.join(commands) )
shellfile.close()
chmod( filename, 0775 )
pop = Popen( ['sh', filename], \
stdout = open( "%s/stdout.txt" % output_dir, 'wb' ), \
stderr = open( "%s/std.err" % output_dir, 'wb' ) )
pop.wait()
print 'snpeff Popen finished'
def run(self, i="", o="", args={'run_locally':True}) :
if not i : i = self.input_file
if not o : o = self.output_dir
run_locally = args['run_locally']
#-i : input
#-o : output
#-d : variation db directory
#-c : coding info directory
snp_exec = "./SIFT_exome_nssnvs.pl" #% (globes.SIFT_BIN)
snp_exec_and_args = [ snp_exec, \
'-i', i, \
'-o', o, \
'-d', \
'%s/db/Human_db_37' % (globes.SIFT_HOME), \
'-A', '1', \
'-B', '1', \
'-C', '1', \
'-J', '1', \
'-K', '1', \
'-L', '1']
indel_exec = ['perl', "%s/SIFT_exome_indels.pl" % (globes.SIFT_BIN)]
indel_exec_and_args = \
indel_exec + \
['-i', i, \
'-o', o, \
'-c', \
'%s/coding_info/Homo_sapien_37' % (globes.SIFT_HOME), \
'-d', \
'%s/db/Human_db_37' % (globes.SIFT_HOME) ]
#choose which version to run
if self.switch == 'snp' :
exec_and_args = snp_exec_and_args
else :
exec_and_args = indel_exec_and_args
if run_locally :
pop = subprocess.Popen(
exec_and_args, \
stdout = open( "%s/stdout" % globes.SIFT_OUTPUT, 'wb' ), \
stderr = open( "%s/stderr"% globes.SIFT_OUTPUT, 'wb' ) )
pop.wait()
else :
params = {'out' : 'sift_out.txt' , \
'err' : 'sift_err.txt' }
commands = ['cd %s' % globes.SIFT_BIN, ' '.join( exec_and_args )]
batchJob = batch.writeBatchFile( "sift_%s.csh" % self.switch, commands )
batchJob.submit()
