if (args.covar_number is not None) and (args.covar is None):
raise ValueError('Covariate number specified without a covariate file')
if (args.keep is not None) and (args.remove is not None):
raise ValueError(
'Specifying both \'--keep\' and \'--remove\' is redundant. Please verify.'
)
if (args.extract is not None) and (args.exclude is not None):
raise ValueError(
'Specifying both \'--extract\' and \'--exclude\' is redundant. Please verify.'
)
# get R if not provided
if args.r_ex == None or args.r_ex == "None":
args.r_ex = find_from_path('R', 'R')
### print settings in use
print 'Basic Settings:'
print '--bfile ' + str(args.bfile)
print '--out ' + str(args.out)
print '--addout ' + str(args.addout)
if args.no_cleanup:
print '--no-cleanup ' + str(args.no_cleanup)
print '\nCovariates:'
print '--covar ' + str(args.covar)
if args.covar is not None:
print ' '.join(cov_num_txt)
if args.pheno is not None and str(args.pheno) != "None":
print '--pheno ' + str(args.pheno)
conf_file = os.environ['HOME'] + "/ricopili.conf"
configs = read_conf(conf_file)
plinkx = configs['p2loc'] + "plink"
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
# get variables from path as needed
# - Rscript (if unspecified)
# - IBD plotting script
# - PCA plotting script (optional)
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_from_path('Rscript', 'Rscript')
Rplotibdx = find_from_path('plot_reap_ibd.Rscript', 'IBD plotting script')
if plot_pca:
Rplotpcax = find_from_path('plot_pca.Rscript', 'PCA plotting script')
# verify executables
test_exec(plinkx, 'Plink')
test_exec(args.rscript_ex, 'Rscript')
test_exec(args.admixture_ex, 'ADMIXTURE')
test_exec(args.reap_ex, 'REAP')
# pca file
if plot_pca:
assert os.path.isfile(
rport = int(args.port)
# sanity check covariate specification, keep/exclude and extract/exclude
if (args.covar_number is not None) and (args.covar is None):
raise ValueError('Covariate number specified without a covariate file')
if (args.keep is not None) and (args.remove is not None):
raise ValueError('Specifying both \'--keep\' and \'--remove\' is redundant. Please verify.')
if (args.extract is not None) and (args.exclude is not None):
raise ValueError('Specifying both \'--extract\' and \'--exclude\' is redundant. Please verify.')
# get R if not provided
if args.r_ex == None or args.r_ex == "None":
args.r_ex = find_from_path('R', 'R')
### print settings in use
print 'Basic Settings:'
print '--bfile '+str(args.bfile)
print '--out '+str(args.out)
print '--addout '+str(args.addout)
if args.no_cleanup:
print '--no-cleanup '+str(args.no_cleanup)
print '\nCovariates:'
print '--covar '+str(args.covar)
if args.covar is not None:
print ' '.join(cov_num_txt)
if args.pheno is not None and str(args.pheno) != "None":
print '--pheno '+str(args.pheno)
# not getting R here since ricopili.conf currently relies on platform info
conf_file = os.environ['HOME']+"/ricopili.conf"
configs = read_conf(conf_file)
plinkx = configs['p2loc']+"plink"
smartpcax = configs['eloc']+"/smartpca"
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
# find required files
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_from_path("Rscript", 'Rscript')
Rplotpcax = find_from_path("plot_pca.Rscript", 'PCA plotting script')
# test executables
test_exec(args.primus_ex, 'PRIMUS')
test_exec(plinkx, 'Plink')
test_exec(smartpcax, 'Eigensoft smartpca')
test_exec(args.rscript_ex, 'Rscript')
print '\n'
print '############'
print 'Begin!'
### read plink loc from config
# not getting R here since ricopili.conf currently relies on platform info
conf_file = os.environ['HOME'] + "/ricopili.conf"
configs = read_conf(conf_file)
plinkx = configs['p2loc'] + "plink"
smartpcax = configs['eloc'] + "/smartpca"
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
# find required files
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_from_path("Rscript", 'Rscript')
Rplotpcax = find_from_path("plot_pca.Rscript", 'PCA plotting script')
# test executables
test_exec(args.primus_ex, 'PRIMUS')
test_exec(plinkx, 'Plink')
test_exec(smartpcax, 'Eigensoft smartpca')
test_exec(args.rscript_ex, 'Rscript')
print '\n'
print '############'
print 'Begin!'
print '############'
####################################
warn("Setting --snp-chunk to a multiple of 100 is NOT recommended currently, due to potential plink --R errors.")
#############
print '\n...Reading ricopili config file...'
#############
### read plink loc from config
conf_file = os.environ['HOME']+"/ricopili.conf"
configs = read_conf(conf_file)
plinkx = configs['p2loc']+"plink"
if args.model == 'gmmat' or args.model == 'gmmat-fam':
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_from_path('Rscript', 'Rscript')
#############
print '\n...Checking dependencies...'
#############
# TODO: here
print '\n'
configs = read_conf(conf_file)
plinkx = configs['p2loc']+"plink"
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
# get variables from path as needed
# - Rscript (if unspecified)
# - IBD plotting script
# - PCA plotting script (optional)
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_from_path('Rscript', 'Rscript')
Rplotibdx = find_from_path('plot_reap_ibd.Rscript', 'IBD plotting script')
if plot_pca:
Rplotpcax = find_from_path('plot_pca.Rscript', 'PCA plotting script')
# verify executables
test_exec(plinkx, 'Plink')
test_exec(args.rscript_ex, 'Rscript')
test_exec(args.admixture_ex, 'ADMIXTURE')
test_exec(args.reap_ex, 'REAP')
# pca file
if plot_pca:
assert os.path.isfile(args.plot_admix_pca), "PCA file does not exist (%r)" % args.plot_admix_pca