def create_command(lz_cmdlist, outfolder, logname, chromosome=None):
cmd_list = ["python lz_meta.py"]
cmd_list.extend(lz_cmdlist)
if chromosome is not None:
c_cmd = ["--chromosome",str(chromosome)]
cmd_list.extend(c_cmd)
#locate log folder
lf = pc_toolbox.log_folder(outfolder)
log_file = os.path.join(lf,logname)
#add log command
t_cmd = ["2>&1|tee",log_file]
cmd_list.extend(t_cmd)
cmd = ' '.join(cmd_list)
print ('My log file is {0} and my command is {1}'.format(log_file,cmd))
return cmd
def create_command(script_loc , pheno_tag=None):
global chromosome,range_start_bp,range_end_bp,plink_test
global p_bound, pheno_loc, c_interval, chrband, build
global output_folder, maxloops, out_flag, condition_list, interrupt
cmd_list = ["python pc_workhorse.py","--chromosome",chromosome,
"--from-bp", str(range_start_bp),"--to-bp", str(range_end_bp),
"--pbound",str(p_bound), "--test", plink_test,
"--script", script_loc, "--outfolder",output_folder,
"--loop",str(maxloops), "--build",build]
## if interrupt:
## cmd_list.extend(['--interrupt'])
of = ""
if out_flag is not None:
of = '_'+out_flag
f_cmd = ["--flag",out_flag]
cmd_list.extend(f_cmd)
logname = ""
log_start = 'Chr'+chromosome+'_'
## if refgene is not None:
## r_cmd = ["--refgene",refgene]
## cmd_list.extend(r_cmd)
if chrband is None:
log_start = 'Chr'+chromosome+'_'
if refgene is None:
r_start = convert_bp_to_mb(range_start_bp)
r_end = convert_bp_to_mb(range_end_bp)
logname =log_start + r_start + '-'+r_end+of
else:
logname = log_start + refgene+of
else:
logname = chrband + of
b_cmd = ["--chrband",chrband]
cmd_list.extend(b_cmd)
lf = pc_toolbox.log_folder(output_folder)
#log_file = os.path.join(lf,log)
if pheno_tag is not None:
logname = logname + '_'+pheno_tag
p_cmd = ["--pheno-tag",pheno_tag]
cmd_list.extend(p_cmd)
ci_cmd = []
if c_interval is None and plink_test in ('logistic',
'linear','assoc',
'fisher'):
c_interval = C_INTERVAL
if c_interval is not None:
ci_cmd = ["--ci",str(c_interval)]
cmd_list.extend(ci_cmd)
t_cmd = []
if condition_list is None:
log = logname + '.log'
log_file = os.path.join(lf,log)
t_cmd = ["2>&1|tee",log_file]
elif interrupt:
cmd_list.extend(['--interrupt'])
c_cmd = ["--condition-list",condition_list]
cmd_list.extend(c_cmd)
if '~' in condition_list:
log = logname + '~.log'
else:
log = logname + '.log'
log_file = os.path.join(lf,log)
t_cmd = ["2>&1|tee -a",log_file]
else:
c_cmd = ["--condition-list",condition_list]
cmd_list.extend(c_cmd)
log = logname + '~.log'
log_file = os.path.join(lf,log)
t_cmd = ["2>&1|tee",log_file]
#t_cmd = ["2>&1|tee",log_file]
cmd_list.extend(t_cmd)
cmd = ' '.join(cmd_list)
print ('My log file is {0} and my command is {1}'.format(log_file,cmd))
return cmd
