print '--sleep ' + str(args.sleep)
print '--mem-req ' + str(args.mem_req)
print '--threads ' + str(args.threads)
if args.full_pipe:
print '--full-pipe'
if str(args.addout) != '' and args.addout is not None:
outdot = str(args.out) + '.' + str(args.addout)
else:
outdot = str(args.out)
#############
print '\n...Checking dependencies...'
#############
plinkx = find_exec('plink', key='p2loc')
shapeit_ex = find_exec('shapeit', key='shloc')
if args.ref_dir is not None:
# verify exists
assert os.path.isdir(
args.ref_dir
), "Failed to find imputation reference directory %s" % args.ref_dir
# prepend to references accordingly
args.ref_maps = str(args.ref_dir) + '/' + args.ref_maps
args.ref_haps = str(args.ref_dir) + '/' + args.ref_haps
args.ref_legs = str(args.ref_dir) + '/' + args.ref_legs
args.ref_samps = str(args.ref_dir) + '/' + args.ref_samps
args.ref_info = str(args.ref_dir) + '/' + args.ref_info
print '\nAnalysis Subset:'
if args.keep is not None:
print '--keep ' + str(args.keep)
else:
print '--remove ' + str(args.remove)
if args.extract is not None:
print '--extract ' + str(args.extract)
else:
print '--exclude ' + str(args.exclude)
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
plinkx = find_exec('plink', key='p2loc')
# verify bfiles are files, not paths
assert '/' not in args.bfile, "--bfile must specify only a file stem, not a path"
# verify input files exist
if args.covar is not None:
assert os.path.isfile(
args.covar), "Covariate file does not exist (%r)" % args.covar
if args.keep is not None:
assert os.path.isfile(
args.keep), "ID inclusion file does not exist (%r)" % args.keep
if args.remove is not None:
assert os.path.isfile(
args.remove), "ID exclusion file does not exist (%r)" % args.remove
if args.extract is not None:
print '--full-pipe'
#############
print '\n...Checking dependencies...'
#############
# get cluster configuration
# needed for specifying logfile names with clust_conf['log_task_id']
conf_file = os.environ['HOME']+"/picopili.conf"
configs = read_conf(conf_file)
cluster = configs['cluster']
clust_conf = read_clust_conf()
# from config
impute_ex = find_exec('impute2',key='i2loc')
shapeit_ex = find_exec('shapeit',key='shloc')
# get directory containing current script
# (to get absolute path for scripts)
rp_bin = os.path.dirname(os.path.realpath(__file__))
chunker_ex = rp_bin+'/chunk_snps.py'
test_exec(chunker_ex,'picopili chunking script')
if args.ref_dir is not None:
# verify exists
assert os.path.isdir(args.ref_dir), "Failed to find imputation reference directory %s" % args.ref_dir
# prepend to references accordingly
args.ref_maps = str(args.ref_dir) +'/' + args.ref_maps
args.ref_haps = str(args.ref_dir) +'/' + args.ref_haps
other_pch = "4"
# print settings
print 'Using settings:'
print '--bfile ' + args.bfile
print '--out ' + args.out
print '--rel-th ' + str(args.rel_th)
print '--npcs ' + str(args.npcs)
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
# from config
plinkx = find_exec('plink', key='p2loc')
smartpcax = find_exec('smartpca', key='eloc')
# if unspecified
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_exec("Rscript", key='rscloc')
if args.primus_ex == None or args.primus_ex == "None":
args.primus_ex = find_exec("run_PRIMUS.pl", key='priloc')
# get directory containing current script
# (to get absolute path for scripts)
rp_bin = os.path.dirname(os.path.realpath(__file__))
Rplotpcax = str(rp_bin) + '/plot_pca.Rscript'
# test executables
print '--exclude'
# print '--info-th'
# print '--rserve-active'
print '\n'
if int(args.snp_chunk) % 100 == 0:
warn("Setting --snp-chunk to a multiple of 100 is NOT recommended currently, due to potential plink --R errors.")
#############
print '\n...Checking dependencies...'
#############
plinkx = find_exec('plink',key='p2loc')
if args.model == 'gmmat' or args.model == 'gmmat-fam':
if args.rscript_ex == None or args.rscript_ex == "None":
args.rscript_ex = find_exec('Rscript', key='rscloc')
if args.model == 'gee' or args.model == 'dfam':
if args.rplink_ex is None or args.rplink_ex == "None":
args.rplink_ex = find_exec('plink',key='rplloc')
if args.model == 'gee':
if args.rserve_ex is None or args.rserve_ex == "None":
args.rserve_ex = find_exec('Rserve',key='rservloc')
# get cluster configuration
print '\nSoftware Settings:'
#if args.rserve_active:
# print '--rserve-active '+str(args.rserve_active)
#else:
print '--r-ex ' + str(args.r_ex)
print '--rplink-ex ' + str(args.rplink_ex)
print '--rserve-ex ' + str(args.rserve_ex)
print '--port ' + str(args.port)
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
if args.rplink_ex is None or args.rplink_ex == "None":
args.rplink_ex = find_exec('plink', key='rplloc')
# get R if not provided
if args.r_ex == None or args.r_ex == "None":
args.r_ex = find_from_path('R', 'R')
# if still fail, try config
if args.r_ex is None or args.r_ex == "None":
args.r_ex = find_exec('R', key='rloc')
if args.rserve_ex is None or args.rserve_ex == "None":
args.rserve_ex = find_exec('Rserve', key='rservloc')
# verify executables
test_exec(args.rplink_ex, 'Plink')
test_exec(args.r_ex, 'R')
if args.extract is not None:
print '--extract ' + str(args.extract)
else:
print '--exclude ' + str(args.exclude)
print '\nSoftware Settings:'
print '--rplink-ex ' + str(args.rplink_ex)
#############
print '\n...Checking dependencies...'
# check exists, executable
#############
# R-compatible plink
if args.rplink_ex is None or args.rplink_ex == "None":
args.rplink_ex = find_exec('plink', key='rplloc')
test_exec(args.rplink_ex, 'Plink')
# verify bfiles are files, not paths
assert '/' not in args.bfile, "--bfile must specify only a file stem, not a path"
# verify input files exist
if args.keep is not None:
assert os.path.isfile(
args.keep), "ID inclusion file does not exist (%r)" % args.keep
if args.remove is not None:
assert os.path.isfile(
args.remove), "ID exclusion file does not exist (%r)" % args.remove
if args.extract is not None:
assert os.path.isfile(
if args.use_exemplars:
print '--min-exemplar ' + str(args.min_exemplar)
if args.admix_q is not None and args.admix_q != "":
print '--admix-q ' + args.admix_q
print '--prop-th ' + str(args.prop_th)
print '--min-exemplar ' + str(args.min_exemplar)
print '--min-rel ' + str(args.min_rel)
if args.plot_admix_pca is not None and args.plot_admix_pca != "":
print '--plot-admix-pca ' + str(args.plot_admix_pca)
#############
print '\n...Checking dependencies...'
# find, check exists, executable
#############
plinkx = find_exec('plink', key='p2loc')
if args.admixture_ex is None or args.admixture_ex == "None":
args.admixture_ex = find_exec('admixture', key='admloc')
else:
test_exec(args.admixture_ex, 'ADMIXTURE')
if args.rscript_ex is None or args.rscript_ex == "None":
args.rscript_ex = find_exec('Rscript', key='rscloc')
else:
test_exec(args.rscript_ex, 'Rscript')
if args.reap_ex is None or args.reap_ex == "None":
args.reap_ex = find_exec('REAP', key='reaploc')
else:
test_exec(args.reap_ex, 'REAP')