def ParseIndList(ids):
id_list = []
if os.path.isfile(ids):
file = open(ids)
for line in file:
words = line.strip().split()
ExitIf(
"%s:%s Individual file lists must contain " %
(line.strip(), len(words)) +
"(exactly 2 columns (first two from ped columns)",
len(words) != 2)
id_list.append(":".join(words[0:2]))
else:
id_list = ids.split(",")
return id_list
def split_mach_jobs(args, filename):
"""Parse the MACH file and generate the list of jobs.
:param args: Arguments from parseargs
:param filename: name of file containing list of mach dosage files
:return jobs to be run
"""
max_snp_count = args.snps_per_job
job_list = {}
cur = None
last_pos = None
job_string = ""
job_name = ""
mach_count = 1
if args.mach_count:
mach_count = args.mach_count
ExitIf(
"mvmany doesn't support splitting mach jobs into pieces at this time",
max_snp_count > 1)
dosage_files = []
for line in open(filename):
dosage_files.append(line.strip().split("/")[-1].split(".")[0])
dosage_files.append(".".join(
line.strip().split()[-1].split("/")[-1].split(".")[0:-1]))
file_count = len(dosage_files)
job_count = int(math.ceil(float(file_count) / mach_count))
for job_num in range(job_count):
job_idx = job_num * mach_count + 1
job_string = "--mach-count %d --mach-offset %d" % (mach_count, job_idx)
job_name = "job%04d-%s" % (job_num + 1, dosage_files[job_idx - 1])
job_list[job_name] = job_string
return job_list
def split_impute_jobs(args, filename):
"""Parse the IMPUTE file and generate the list of jobs.
:param args: parsearg object containing command line arguments
:filename args: file containing the IMPUTE gen files and chromosome numbers
"""
max_snp_count = args.snps_per_job
if args.impute_count:
impute_count = args.impute_count
else:
impute_count = 1
ExitIf(
"mvmany doesn't support splitting IMPUTE jobs into pieces at this time",
max_snp_count > 1)
job_list = {}
gen_files = []
for line in open(filename):
gen_files.append(".".join(
line.strip().split()[-1].split("/")[-1].split(".")[0:-1]))
file_count = len(gen_files)
job_count = int(math.ceil(float(file_count) / impute_count))
for job_num in range(job_count):
job_idx = job_num * impute_count + 1
job_string = "--impute-offset %d --impute-count %d" % (job_idx,
impute_count)
job_name = "job%04d-%s" % (job_num + 1, gen_files[job_idx - 1])
job_list[job_name] = job_string
print job_string
return job_list
# For now, let's not deal with the complexity of splitting chromosomes in IMPUTE
poscol = 2
cur = None
last_pos = None
job_string = ""
job_name = ""
file_index = 0
for line in open(filename):
chr, genfile = line.strip().split()
if max_snp_count > 0:
locus_index = 0
last_pos = 1
for locus in open(genfile):
if locus_index >= max_snp_count - 1:
rsid, pos = locus.split()[1:2]
job_name = "chr%d_%d" % (chr, last_pos)
job_string = "--chr %s --from-bp %d --to-bp %d" % (
chr, last_pos, pos)
last_pos = pos + 1
job_list[job_name] = job_string
locus_index = 0
if cur is None:
cur = pos
for line in sys_call("cut -f 1,%d %s" % (poscol, chrom_file)):
chrom, pos = [int(x) for x in line.split()]
if cur is None: # First line observed
cur = chrom
job_string = "--chr %d --from-bp %d" % (chrom, pos)
job_name = "Chr%d_%d-" % (chrom, pos)
snp_count = 0
elif cur != cur: # Changed chromosome
job_string += " --to-bp %d" % (last_pos)
job_name += str(last_pos)
job_list[job_name] = job_string
cur = chrom
job_string = "--chr %d --from-bp %d" % (chrom, pos)
job_name = "Chr%d_%d-" % (chrom, pos)
snp_count = 0
# create new job based on snp count
elif snp_count < max_snp_count:
snp_count += 1
else:
job_string += " --to-bp %d" % (last_pos)
job_name += str(last_pos)
job_list[job_name] = job_string
job_string = "--chr %d --from-bp" % (chrom, pos)
job_name = "Chr%d_%d-" % (chrom, pos)
snp_count = 0
last_pos = pos
if job_string != "":
job_string += " --to-bp %d" % (last_pos)
job_name += str(last_pos)
job_list[job_name] = job_string
return job_list
from libgwas.pheno_covar import PhenoCovar
from libgwas.exceptions import ReportableException
import libgwas.pedigree_parser as pedigree_parser
import libgwas.transposed_pedigree_parser as transposed_pedigree_parser
import libgwas.bed_parser as bed_parser
import meanvar.mv_esteq as mv_esteq
from libgwas import BuildReportLine
from libgwas import impute_parser
from libgwas import mach_parser
import libgwas.standardizer
import meanvar.mvstandardizer
from libgwas import ExitIf
__version__ = meanvar.__version__
ExitIf("mvtest.py requires python 2.7.x to run", sys.version_info < (2, 7))
libgwas.standardizer.set_standardizer(meanvar.mvstandardizer.Standardizer)
"""usage: mvtest.py [-h] [-v] [--vall] [--chr N] [--snps SNPS] [--from-bp START]
[--to-bp END] [--from-kb START] [--to-kb END]
[--from-mb START] [--to-mb END] [--exclude EXCLUDE]
[--keep KEEP] [--remove REMOVE] [--file FILE] [--ped PED]
[--map MAP] [--map3] [--no-sex] [--no-parents] [--no-fid]
[--no-pheno] [--liability] [--bfile BFILE] [--bed BED]
[--bim BIM] [--fam FAM] [--tfile TFILE] [--tped TPED]
[--tfam TFAM] [--compressed] [--impute IMPUTE]
[--impute-fam IMPUTE_FAM] [--impute-offset IMPUTE_OFFSET]
[--impute-count IMPUTE_COUNT] [--impute-uncompressed]
[--impute-encoding {additive,dominant,recessive,genotype}]
[--impute-info-ext IMPUTE_INFO_EXT]
[--impute-gen-ext IMPUTE_GEN_EXT]