def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("--program",
dest="program",
type="choice",
choices=["plink2", "gcta", "plinkdev"],
help="program to execute genome-wide analysis")
parser.add_option("--input-file-pattern",
dest="infile_pattern",
type="string",
help="file prefix that identifies a group of files")
parser.add_option("--input-file-format",
dest="file_format",
type="choice",
choices=[
"plink", "plink_binary", "oxford", "oxford_binary",
"vcf", "GRM_binary", "GRM_gz", "GRM_plink"
],
help="format of input files")
parser.add_option("--phenotypes-file",
dest="pheno_file",
type="string",
help="text file of additional phenotypes")
parser.add_option("--pheno",
dest="pheno",
type="string",
help="either phenotype file column header or number")
parser.add_option("--covariates-file",
dest="covariate_file",
type="string",
help="file containing covariates. Used as the "
"continuous covariates in GCTA-based analyses")
parser.add_option("--covariate-column",
dest="covar_col",
type="string",
help="column number(s) or header(s) to include in "
"association model")
parser.add_option("--discrete-covariates-file",
dest="covariate_discrete",
type="string",
help="file containing discrete covariates "
"to adjust for in GCTA-based analyses")
parser.add_option("--association-model",
dest="assoc_model",
type="choice",
choices=["recessive", "dominant", "genotype"],
help="model to report from association analysis")
parser.add_option("--method",
dest="method",
type="choice",
choices=[
"association", "summary", "format", "matrix", "reml",
"bivariate_reml", "pca", "lmm", "simulation",
"epistasis", "ld", "estimate_haplotypes"
],
help="method to apply to genome-wide data")
parser.add_option("--reml-method",
dest="reml_method",
type="choice",
choices=[
"standard", "priors", "reml_algorithm",
"unconstrained", "GxE", "LRT", "BLUP_EBV", "snpBLUP",
"no_residual", "fixed_cor"
],
help="method for REML estimate of heritability method "
"including either single or dual phenotypes")
parser.add_option("--reml-parameters",
dest="reml_param",
type="string",
help="comma separated list of parameters to pass to "
"REML variance components analysis")
parser.add_option("--prevalence",
dest="prevalence",
type="float",
help="binary trait prevalence in a cohort study. "
"Used to estimate h2 on the liability threshold "
"scale.")
parser.add_option("--lmm-method",
dest="lmm_method",
type="choice",
choices=["standard", "loco", "no_covar"],
help="type of linear mixed model analysis to run")
parser.add_option("--grm-prefix",
dest="grm_prefix",
type="string",
help="prefix of the pre-computed GRM files to use "
"in the linear mixed model analysis")
parser.add_option(
"--epistasis-method",
dest="epi_method",
type="choice",
choices=["fast_epistasis", "epistasis", "two_locus", "adjusted"],
help="epistasis method to use")
parser.add_option("--epistasis-parameter",
dest="epi_param",
type="string",
help="modifiers of epistasis functions")
parser.add_option("--epistasis-threshold",
dest="epi_sig",
type="string",
help="statistical significance threshold for counting "
"interactions")
parser.add_option("--epistasis-report-threshold",
dest="epi_report",
type="string",
help="threshold used to count the "
"proportion of statistically significant interactions")
parser.add_option("--set-file",
dest="set_file",
type="string",
help="file containing variant sets as per Plink "
".set file specification")
parser.add_option("--set-method",
dest="set_method",
type="choice",
choices=["set-by-all", "set-by-set"],
help="set method to use when `set_file` provided")
parser.add_option("--principal-components",
dest="num_pcs",
type="int",
help="the number of principal components to output")
parser.add_option("--matrix-shape",
dest="matrix_shape",
type="choice",
choices=["triangle", "square", "square0"],
help="output matrix shape.",
default="triangle")
parser.add_option("--matrix-compression",
dest="matrix_compress",
type="choice",
choices=["gz", "bin", "bin4"],
help="compression to apply to output matrix")
parser.add_option("--matrix-form",
dest="matrix_form",
type="choice",
choices=["distance", "grm"],
help="type of relationship matrix to calculate")
parser.add_option(
"--matrix-metric",
dest="matrix_metric",
type="choice",
choices=["fhat", "cov", "ibc2", "ibc3", "ibs", "genomic", "hamming"],
help="value to calculate for diagonal elements of the "
"grm. Default is fhat for grm and hamming for distance.")
parser.add_option(
"--matrix-options",
dest="matrix_options",
type="string",
help="modifiers of matrix output, see plink documentation "
"for details")
parser.add_option("--association-method",
dest="assoc_method",
type="choice",
choices=["linear", "logistic", "assoc", "qassoc"],
help="association analysis to run")
parser.add_option(
"--permutation",
dest="permutation",
action="store_true",
help="perform association testing by permutation analysis")
parser.add_option("--repeats",
dest="n_perms",
type="int",
help="number of repetitions for permutation analysis")
parser.add_option("--association-options",
dest="assoc_option",
type="string",
help="association analysis modifiers")
parser.add_option("--format-method",
dest="format_method",
type="choice",
choices=[
"change_format", "change_missing_values",
"update_variants", "update_samples", "flip_strands",
"flip_scan", "sort", "merge", "find_duplicates"
],
help="file formatting to apply to input files")
parser.add_option("--format-parameter",
dest="format_param",
type="string",
help="formatting parameter, where appropriate")
parser.add_option(
"--reformat-type",
dest="reformat",
type="choice",
choices=["plink", "plink_binary", "oxford", "oxford_binary", "raw"],
help="new format of input files to be reformatted to")
parser.add_option("--apply-missing",
dest="apply_missing",
type="choice",
choices=["genotype", "phenotype"],
help="genotype or phenotype missing values to alter")
parser.add_option("--update-variant-attribute",
dest="variant_update",
type="choice",
choices=[
"variant_ids", "missing_id", "chromosome",
"centimorgan", "name", "alleles", "map"
],
help="update variant attributes")
parser.add_option("--update-sample-attribute",
dest="sample_update",
type="choice",
choices=["sample_ids", "parents", "gender"],
help="sample attributes to be updated")
parser.add_option("--strand-flip-subset",
dest="flip_subset",
action="store_true",
help="apply strand flipping to a subset of samples")
parser.add_option("--flip-scan-type",
dest="scan_param",
type="choice",
choices=["default", "window", "threshold"],
help="strand flipping scan to apply to SNPs")
parser.add_option("--sort-type",
dest="sort_type",
type="choice",
choices=["none", "natural", "ascii", "file"],
help="sort type to input files")
parser.add_option("--merge-file-format",
dest="merge_format",
type="choice",
choices=["plink", "plink_binary"],
help="format of input files to be merged")
parser.add_option(
"--merge-mode",
dest="merge_mode",
type="choice",
choices=[
"default", "original_missing", "new_nonmissing", "no_overwrite",
"force", "report_all", "report_nonmissing"
],
help="merge mode to apply to dealing with merge conflicts")
parser.add_option("--duplicates-method",
dest="dup_method",
type="choice",
choices=["same_ref", "id_match", "suppress_first"],
help="method for identifying and dealing with duplicate "
"variants")
parser.add_option("--summary-method",
dest="summary_method",
type="choice",
choices=[
"allele_frequency", "missing_data", "hardy_weinberg",
"mendel_errors", "inbreeding", "gender_checker",
"wrights_fst", "case_control_fst"
],
help="summary statistics to calculate")
parser.add_option("--summary-parameter",
dest="sum_param",
type="string",
help="optional parameters that can be passed to summary "
"statistics methods")
parser.add_option("--haplotype-frequency",
dest="filt_haplotype_frequency",
type="string",
help="min allele frequency for SNPs to be "
"considered for a haplotype")
parser.add_option("--haplotype-size",
dest="filt_haplotype_size",
type="string",
help="maximum genomic size of "
"haplotypes")
parser.add_option("--ld-statistic",
dest="ld_stat",
type="choice",
choices=["r", "r2"],
help="compute either the raw "
"inter variant allele count correlation, R, or the "
"squared correlation, R^2")
parser.add_option("--ld-min",
dest="ld_min",
type="string",
help="minimum value to report for pair-wise LD "
"calculations. Beware output files may be very "
"large if `ld_min` is very small.")
parser.add_option("--ld-window",
dest="ld_window",
type="string",
help="distance between SNPs, beyond which LD will "
"not be calculated")
parser.add_option("--ld-format-output",
dest="ld_shape",
type="choice",
choices=["square", "table", "triangle", "square0"],
help="output either as table, or matrix format with a "
"specific shape.")
parser.add_option(
"--genotype-rate",
dest="filt_genotype_rate",
type="string",
help="genotyping rate threshold. SNPs below this threshold "
"will be excluded from analysis")
parser.add_option("--indiv-missing",
dest="filt_missingness",
type="string",
help="individual missingness rate. Individuals below "
"this threshold will be excluded from analysis")
parser.add_option("--hardy-weinberg",
dest="filt_hwe",
type="string",
help="hardy-weinberg p-value threshold for SNPs. SNPs "
"with a 2df chisquared p-value below this will be "
"filtered out")
parser.add_option(
"--min-allele-frequency",
dest="filt_min_allele_frequency",
type="string",
help="only include SNPs with an allele frequency equal to "
"or above this threshold")
parser.add_option(
"--max-allele-frequency",
dest="filt_max_allele_frequency",
type="string",
help="only include SNPs with an allele frequency equal to "
"or below this threshold")
parser.add_option(
"--mendelian-error",
dest="filt_mendelian_error",
type="string",
help="exclude individuals/trios with mendelian errors that "
"exceed this value")
parser.add_option("--keep-individuals",
dest="filt_keep",
type="string",
help="a file containing individuals IDs to keep, "
"one per row")
parser.add_option("--remove-individuals",
dest="filt_remove",
type="string",
help="a file of individual IDs to remove, one per row")
parser.add_option("--min-quality-score",
dest="filt_min_qaul_score",
type="string",
help="reset the minimum low bound of quality scores for "
"variants in a VCF file. Default is 0")
parser.add_option(
"--max-quality-score",
dest="filt_max_qual_score",
type="string",
help="reset the maximum upper bound of quality scores for "
"a VCCF file. Default is Inf")
parser.add_option("--allow-no-gender",
dest="filt_allow_no_sex",
type="string",
help="allow individuals with gender missing")
parser.add_option("--enforce-gender",
dest="filt_enforce_sex",
type="string",
help="only include individuals with non-missing gender "
"information")
parser.add_option("--subset-filter",
dest="filt_subset_filter",
type="choice",
choices=[
"cases", "controls", "males", "females", "founders",
"nonfounders"
],
help="only apply filters to the specific subset of "
"individuals supplied")
parser.add_option(
"--extract-snps",
dest="filt_extract",
type="string",
help="text file of variant IDs to include in the analysis, "
"ignoring all others")
parser.add_option("--exclude-snps",
dest="filt_exclude",
type="string",
help="a file of variant IDs to exclude from analysis")
parser.add_option("--restrict-chromosome",
dest="filt_chromosome",
type="string",
help="restict analysis to either a single chromosome, "
"or a comma-separated list of chromosomes")
parser.add_option("--exclude-chromosomes",
dest="filt_exclude_chromosome",
type="string",
help="exclude all variants on these "
"chromosome(s)")
parser.add_option(
"--autosome-only",
dest="filt_autosome",
action="store_true",
help="if present only autosomal variants will be analysed")
parser.add_option(
"--pseudo-autosome",
dest="filt_pseudo_autosome",
action="store_true",
help="include on the pseudo-autosomal region of chromosome X")
parser.add_option("--ignore-indels",
dest="filt_ignore_indels",
action="store_true",
help="only include bi-allelic single nucleotide "
"variants in analysis")
parser.add_option(
"--snp-range",
dest="filt_snp_bp_range",
type="string",
help="comma separated list of from, to genome co-ordinates "
"within which to include variants for analysis")
parser.add_option(
"--conditional-snp",
dest="filt_conditional_snp",
type="string",
help="condition the analysis on this SNP ID. Can only be "
"used in the linear and logistic regression models.")
parser.add_option("--snp-id-range",
dest="filt_snp_id_range",
type="string",
help="comma separate list of IDs from, to within which "
"to include variants for analysis.")
parser.add_option("--snp-id",
dest="filt_specific_snp",
type="string",
help="include a single snp in the analysis given by "
"it's variant ID.")
parser.add_option("--exclude-variant",
dest="filt_exclude_snp",
type="string",
help="exclude a single variant from the analysis, "
"given by it's variant ID")
parser.add_option(
"--covariate-filter",
dest="filt_covariate_filter",
type="string",
help="covariate column headers or column numbers on which "
"to filter on. Requries --covariate-file")
parser.add_option(
"--filter-parameter",
dest="param",
type="string",
help="parameter values to be passed to filtering function")
parser.add_option("--window-size",
dest="window_size",
type="string",
help="alters the behaviour of the --snp-range and "
"--include/exclude snp options. variants within +/- "
"half * window_size (kb) are included")
parser.add_option(
"--range-resolution",
dest="filt_range_resolution",
type="choice",
choices=["bp", "kb", "mb"],
help="alters the (from, to) range resolution to either bp, "
"kb or mb")
parser.add_option(
"--output-file-pattern",
dest="out_pattern",
type="string",
help="output file pattern prefix. file suffixes are dependent "
"on the task executed")
parser.add_option("--threads",
dest="threads",
type="int",
help="the number of threads to use for multi-threaded "
"processes")
parser.add_option("--memory",
dest="memory",
type="string",
help="amount of memory to reserve for the task")
parser.add_option("--parallel",
dest="parallel",
type="int",
help="number of jobs to split task into")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
parser.set_defaults(sum_param=None,
dup_method="same_ref",
n_perms=None,
permutation=False,
matrix_shape="triangle",
matrix_options=None,
matrix_compress="gz",
random_seed=random.randint(0, 19999),
sample_update=None,
memory="60G",
parallel=None,
covariate_file=None,
covar_col=None,
epi_report=0.001,
epi_sig=0.001)
if not options.infile_pattern:
infiles = (argv[-1]).split(",")
else:
infiles = options.infile_pattern
# create a new filegroup object
geno_files = gwas.FileGroup(files=infiles,
file_format=options.file_format,
genotype_format="imputed")
if options.pheno_file:
geno_files.set_phenotype(pheno_file=options.pheno_file,
pheno=options.pheno)
else:
pass
# add FileGroup object to the gwas program object
if options.program == "plink2":
gwas_object = gwas.Plink2(files=geno_files)
gwas_object.program_call(infiles=geno_files,
outfile=options.out_pattern)
elif options.program == "plinkdev":
gwas_object = gwas.PlinkDev(files=geno_files)
gwas_object.program_call(infiles=geno_files,
outfile=options.out_pattern)
elif options.program == "gcta":
gwas_object = gwas.GCTA(files=geno_files)
gwas_object.program_call(infiles=geno_files,
outfile=options.out_pattern)
else:
pass
# collect filtering options from options
opt_dict = options.__dict__
filter_keys = [fx for fx in opt_dict.keys() if re.search("filt", fx)]
filter_dict = {k: options.__dict__[k] for k in filter_keys if opt_dict[k]}
# iteratively add genotype filters to GWASProgram object
for fkey in filter_dict:
filt_key = fkey.lstrip("filt_")
filter_value = filter_dict[fkey]
gwas_object.apply_filters(filter_type=filt_key,
filter_value=filter_value)
# handle summary statistics
if options.method == "summary":
if options.summary_method == "allele_frequency":
gwas_object._output_statistics(allele_frequency=options.sum_param)
elif options.summary_method == "hardy_weinberg":
gwas_object._output_statistics(hardy_weinberg=options.sum_param)
elif options.summary_method == "missing_data":
gwas_object._output_statistics(missing_data=options.sum_param)
elif options.summary_method == "mendel_errors":
gwas_object._output_statistics(mendel_errors=options.sum_param)
elif options.summary_method == "inbreeding":
gwas_object._output_statistics(inbreeding=options.sum_param)
elif options.summary_method == "gender_checker":
gwas_object._output_statistics(gender_checker=options.sum_param)
elif options.summary_method == "wrights_fst":
gwas_object._output_statistics(wrights_fst=options.sum_param)
elif options.summary_method == "case_control_fst":
gwas_object._output_statistics(case_control_fst=options.sum_param)
else:
pass
elif options.method == "pca":
gwas_object.PCA(n_pcs=options.num_pcs)
elif options.method == "ld":
gwas_object.calc_ld(ld_statistic=options.ld_stat,
ld_threshold=float(options.ld_min),
ld_shape=options.ld_shape)
elif options.method == "association":
gwas_object.run_association(association=options.assoc_method,
permutation=options.permutation,
n_perms=options.n_perms,
random_seed=options.random_seed,
covariates_file=options.covariate_file,
covariates=options.covar_col)
elif options.method == "estimate_haplotypes":
gwas_object._run_tasks(estimate_haplotypes="haplotype")
elif options.method == "lmm":
gwas_object.mixed_model(lmm_method=options.lmm_method,
grm=options.grm_prefix,
qcovar=options.covariate_file,
dcovar=options.covariate_discrete)
elif options.method == "epistasis":
gwas_object._detect_interactions(
method=options.epi_method,
modifier=options.epi_param,
set_file=options.set_file,
set_mode=options.set_method,
report_threshold=options.epi_report,
sig_threshold=options.epi_sig,
covariates_file=options.covariate_file,
covariates=options.covar_col)
elif options.method == "reml":
gwas_object.reml_analysis(method=options.reml_method,
parameters=options.reml_param,
prevalence=options.prevalence,
qcovariates=options.covariate_file,
discrete_covar=options.covariate_discrete)
elif options.method == "format":
if options.format_method == "change_format":
# adding filtering options to plink requires the --make-bed flag
try:
update_samples = opt_dict["sample_update"]
if update_samples:
E.info("updating samples from %s" % options.format_param)
gwas_object._run_tasks(change_format=options.reformat,
parameter=options.format_param)
gwas_object._run_tasks(
update_samples=options.sample_update,
parameter=options.format_param)
else:
gwas_object._run_tasks(change_format=options.reformat,
parameter=options.format_param)
except KeyError:
gwas_object._run_tasks(change_format=options.reformat,
parameter=options.format_param)
elif options.format_method == "change_missing_values":
gwas_object._run_tasks(change_missing_values=options.apply_missing,
parameter=options.format_param)
elif options.format_method == "update_variants":
gwas_object._run_tasks(update_variants=options.variant_update,
parameter=options.format_param)
gwas_object._run_tasks(change_format=options.file_format)
elif options.format_method == "update_samples":
gwas_object._run_tasks(update_samples=options.sample_update,
parameter=options.format_param)
elif options.format_method == "flip_strands":
if options.flip_subset:
gwas_object._run_tasks(flip_strands="subset",
parameter=options.format_param)
else:
gwas_object._run_tasks(flip_strands="all_samples",
parameter=options.format_param)
elif options.format_method == "flip_scan":
gwas_object._run_tasks(flip_scan=options.scan_param,
parameter=options.format_param)
elif options.format_method == "sort":
gwas_object._run_tasks(sort=options.sort_type,
parameter=options.format_param)
elif options.format_method == "merge":
if options.merge_mode:
gwas_object._run_tasks(merge_mode=options.merge_mode,
parameter=options.format_param)
else:
gwas_object._run_tasks(merge=options.merge_format,
parameter=options.format_param)
elif options.format_method == "find_duplicates":
gwas_object._run_tasks(find_duplicates=options.dup_method,
parameter=options.format_param)
else:
pass
elif options.method == "matrix":
if options.matrix_form == "distance":
if options.matrix_metric == "hamming":
gwas_object.hamming_matrix(shape=options.matrix_shape,
compression=options.matrix_compress,
options=options.matrix_options)
elif options.matrix_metric == "ibs":
gwas_object.ibs_matrix(shape=options.matrix_shape,
compression=options.matrix_compress,
options=options.matrix_options)
elif options.matrix_metric == "genomic":
gwas_object.genome_matrix(shape=options.matrix_shape,
compression=options.matrix_compress,
options=options.matrix_options)
elif options.matrix_form == "grm":
gwas_object.genetic_relationship_matrix(
shape=options.matrix_shape,
compression=options.matrix_compress,
metric=options.matrix_metric,
options=options.matrix_options)
else:
pass
gwas_object.build_statement(infiles=geno_files,
outfile=options.out_pattern,
threads=options.threads,
memory=options.memory,
parallel=options.parallel)
# write footer and output benchmark information.
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("--program",
dest="program",
type="choice",
choices=["plink2", "gcta", "plinkdev"],
help="program to execute genome-wide analysis")
parser.add_option("--input-file-pattern",
dest="infile_pattern",
type="string",
help="file prefix that identifies a group of files")
parser.add_option("--input-file-format",
dest="file_format",
type="choice",
choices=[
"plink", "plink_binary", "oxford", "oxford_binary",
"vcf", "GRM_binary", "GRM_gz"
],
help="format of input files")
parser.add_option("--phenotypes-file",
dest="pheno_file",
type="string",
help="text file of additional phenotypes")
parser.add_option("--pheno",
dest="pheno",
type="string",
help="either phenotype file column header or number")
parser.add_option("--covariates-file",
dest="covariate_file",
type="string",
help="file containing covariates")
parser.add_option("--covariate-column",
dest="covar_col",
type="string",
help="column number(s) or header(s) to include in "
"association model")
parser.add_option("--method",
dest="method",
type="choice",
choices=[
"ld_prune", "summary", "flag_hets",
"remove_relations", "check_gender", "IBD"
],
help="method to apply to genome-wide data")
parser.add_option("--IBD-parameter",
dest="ibd_param",
type="choice",
choices=["norm", "relatives", "full"],
help="param "
"to pass to IBD calculations")
parser.add_option("--principal-components",
dest="num_pcs",
type="int",
help="the number of principal components to output")
parser.add_option("--matrix-shape",
dest="matrix_shape",
type="choice",
choices=["triangle", "square", "square0"],
help="output matrix shape.",
default="triangle")
parser.add_option("--matrix-compression",
dest="matrix_compress",
type="choice",
choices=["gz", "bin", "bin4"],
help="compression to apply to output matrix file",
default="gz")
parser.add_option("--matrix-form",
dest="matrix_form",
type="choice",
choices=["distance", "grm"],
help="type of relationship matrix to calculate")
parser.add_option(
"--matrix-metric",
dest="matrix_metric",
type="choice",
choices=["fhat", "cov", "ibc2", "ibc3", "ibs", "genomic", "hamming"],
help="value to calculate for diagonal elements of the "
"grm. Default is fhat for grm and hamming for distance.")
parser.add_option(
"--matrix-options",
dest="matrix_options",
type="string",
help="modifiers of matrix output, see plink documentation "
"for details")
parser.add_option("--strand-flip-subset",
dest="flip_subset",
action="store_true",
help="apply strand flipping to a subset of samples")
parser.add_option("--flip-scan-type",
dest="scan_param",
type="choice",
choices=["default", "window", "threshold"],
help="strand flipping scan to apply to SNPs")
parser.add_option("--sort-type",
dest="sort_type",
type="choice",
choices=["none", "natural", "ascii", "file"],
help="sort type to input files")
parser.add_option("--merge-file-format",
dest="merge_format",
type="choice",
choices=["plink", "binary_plink"],
help="format of input files to be merged")
parser.add_option(
"--merge-mode",
dest="merge_mode",
type="choice",
choices=[
"default", "original_missing", "new_nonmissing", "no_overwrite",
"force", "report_all", "report_nonmissing"
],
help="merge mode to apply to dealing with merge conflicts")
parser.add_option("--duplicates-method",
dest="dup_method",
type="choice",
choices=["same_ref", "id_match", "suppress_first"],
help="method for identifying and dealing with duplicate "
"variants")
parser.add_option("--summary-method",
dest="summary_method",
type="choice",
choices=[
"allele_frequency", "missing_data", "hardy_weinberg",
"mendel_errors", "inbreeding", "inbreeding_coef",
"gender_checker", "wrights_fst"
],
help="summary statistics to calculate")
parser.add_option("--summary-parameter",
dest="sum_param",
type="string",
help="optional parameters that can be passed to summary "
"statistics methods")
parser.add_option(
"--genotype-rate",
dest="filt_genotype_rate",
type="string",
help="genotyping rate threshold. SNPs below this threshold "
"will be excluded from analysis")
parser.add_option("--indiv-missing",
dest="filt_missingness",
type="string",
help="individual missingness rate. Individuals below "
"this threshold will be excluded from analysis")
parser.add_option("--hardy-weinberg",
dest="filt_hwe",
type="string",
help="hardy-weinberg p-value threshold for SNPs. SNPs "
"with a 2df chisquared p-value below this will be "
"filtered out")
parser.add_option(
"--min-allele-frequency",
dest="filt_min_allele_frequency",
type="string",
help="only include SNPs with an allele frequency equal to "
"or above this threshold")
parser.add_option(
"--max-allele-frequency",
dest="filt_max_allele_frequency",
type="string",
help="only include SNPs with an allele frequency equal to "
"or below this threshold")
parser.add_option(
"--mendelian-error",
dest="filt_mendelian_error",
type="string",
help="exclude individuals/trios with mendelian errors that "
"exceed this value")
parser.add_option("--min-quality-score",
dest="filt_min_qaul_score",
type="string",
help="reset the minimum low bound of quality scores for "
"variants in a VCF file. Default is 0")
parser.add_option(
"--max-quality-score",
dest="filt_max_qual_score",
type="string",
help="reset the maximum upper bound of quality scores for "
"a VCCF file. Default is Inf")
parser.add_option("--allow-no-gender",
dest="filt_allow_no_sex",
type="string",
help="allow individuals with gender missing")
parser.add_option("--enforce-gender",
dest="filt_enforce_sex",
type="string",
help="only include individuals with non-missing gender "
"information")
parser.add_option("--keep-individuals",
dest="filt_keep",
type="string",
help="a file containing individuals IDs to keep, "
"one per row")
parser.add_option("--remove-individuals",
dest="filt_remove",
type="string",
help="a file of individual IDs to remove, one per row")
parser.add_option("--subset-filter",
dest="filt_subset_filter",
type="choice",
choices=[
"cases", "controls", "males", "females", "founders",
"nonfounders"
],
help="only apply filters to the specific subset of "
"individuals supplied")
parser.add_option(
"--extract-snps",
dest="filt_extract",
type="string",
help="text file of variant IDs to include in the analysis, "
"ignoring all others")
parser.add_option("--exclude-snps",
dest="filt_exclude",
type="string",
help="a file of variant IDs to exclude from analysis")
parser.add_option("--restrict-chromosome",
dest="filt_chromosome",
type="string",
help="restict analysis to either a single chromosome, "
"or a comma-separated list of chromosomes")
parser.add_option("--exclude-chromosomes",
dest="filt_exclude_chromosome",
type="string",
help="exclude all variants on these "
"chromosome(s)")
parser.add_option(
"--autosome-only",
dest="filt_autosome",
action="store_true",
help="if present only autosomal variants will be analysed")
parser.add_option(
"--pseudo-autosome",
dest="filt_pseudo_autosome",
action="store_true",
help="include on the pseudo-autosomal region of chromosome X")
parser.add_option("--ignore-indels",
dest="filt_ignore_indels",
action="store_true",
help="only include bi-allelic single nucleotide "
"variants in analysis")
parser.add_option(
"--snp-range",
dest="filt_snp_bp_range",
type="string",
help="comma separated list of from, to genome co-ordinates "
"within which to include variants for analysis")
parser.add_option("--snp-id-range",
dest="filt_snp_id_range",
type="string",
help="comma separate list of IDs from, to within which "
"to include variants for analysis.")
parser.add_option("--snp-id",
dest="filt_specific_snp",
type="string",
help="include a single snp in the analysis given by "
"it's variant ID.")
parser.add_option("--exclude-variant",
dest="filt_exclude_snp",
type="string",
help="exclude a single variant from the analysis, "
"given by it's variant ID")
parser.add_option(
"--covariate-filter",
dest="filt_covariate_filter",
type="string",
help="covariate column headers or column numbers on which "
"to filter on. Requries --covariate-file")
parser.add_option(
"--filter-parameter",
dest="param",
type="string",
help="parameter values to be passed to filtering function")
parser.add_option("--window-size",
dest="window_size",
type="string",
help="alters the behaviour of the --snp-range and "
"--include/exclude snp options. variants within +/- "
"half * window_size (kb) are included")
parser.add_option(
"--range-resolution",
dest="filt_range_resolution",
type="choice",
choices=["bp", "kb", "mb"],
help="alters the (from, to) range resolution to either bp, "
"kb or mb")
parser.add_option(
"--output-file-pattern",
dest="out_pattern",
type="string",
help="output file pattern prefix. file suffixes are dependent "
"on the task executed")
parser.add_option("--threads",
dest="threads",
type="int",
help="the number of threads to use for multi-threaded "
"processes")
parser.add_option("--use-kb",
dest="kb",
action="store_true",
help="if present uses a kb sized window for LD pruning")
parser.add_option("--prune-method",
dest="prune_method",
type="choice",
choices=["R2", "VIF"],
help="type of LD pruning to "
"perform, pair-wise LD or variance inflation factor")
parser.add_option("--step-size",
dest="step",
type="string",
help="step size to advance window by")
parser.add_option("--threshold",
dest="threshold",
type="string",
help="threshold on which to filter results")
parser.add_option("--parallel",
dest="parallel",
type="int",
help="number of jobs to split task into")
parser.add_option("--memory",
dest="memory",
type="string",
help="amount of memory to reserve for the task")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
parser.set_defaults(sum_param=None,
dup_method="same_ref",
matrix_shape="triangle",
matrix_options=None,
matrix_compress="gz",
kb=False,
random_seed=random.randint(0, 19999),
memory="60G",
parallel=None)
if not options.infile_pattern:
infiles = (argv[-1]).split(",")
else:
infiles = options.infile_pattern
# create a new filegroup object
geno_files = gwas.FileGroup(files=infiles,
file_format=options.file_format,
genotype_format="imputed")
if options.pheno_file:
geno_files.set_phenotype(pheno_file=options.pheno_file,
pheno=options.pheno)
else:
pass
# add FileGroup object to the gwas program object
if options.program == "plink2":
gwas_object = gwas.Plink2(files=geno_files)
gwas_object.program_call(infiles=geno_files,
outfile=options.out_pattern)
elif options.program == "plinkdev":
gwas_object = gwas.PlinkDev(files=geno_files)
gwas_object.program_call(infiles=geno_files,
outfile=options.out_pattern)
elif options.program == "gcta":
gwas_object = gwas.GCTA(files=geno_files)
gwas_object.program_call(infiles=geno_files,
outfile=options.out_pattern)
else:
pass
# collect filtering options from options
opt_dict = options.__dict__
filter_keys = [fx for fx in opt_dict.keys() if re.search("filt", fx)]
filter_dict = {k: options.__dict__[k] for k in filter_keys if opt_dict[k]}
# iteratively add all filters to GWASProgram object
for fkey in filter_dict:
filt_key = fkey.replace("filt_", "")
filter_value = filter_dict[fkey]
gwas_object.apply_filters(filter_type=filt_key,
filter_value=filter_value)
# handle summary statistics
if options.method == "ld_prune":
gwas_object._qc_methods(ld_prune=options.prune_method,
kb=True,
window=options.window_size,
step=options.step,
threshold=options.threshold)
elif options.method == "IBD":
# use sum param to pass arguments to ibd estiamte
# these are norm, full or relatitves
gwas_object._qc_methods(ibd=options.ibd_param)
elif options.method == "summary":
if options.summary_method == "allele_frequency":
gwas_object._output_statistics(allele_frequency=options.sum_param)
elif options.summary_method == "hardy_weinberg":
gwas_object._output_statistics(hardy_weinberg=options.sum_param)
elif options.summary_method == "missing_data":
gwas_object._output_statistics(missing_data=options.sum_param)
elif options.summary_method == "mendel_errors":
gwas_object._output_statistics(mendel_errors=options.sum_param)
elif options.summary_method == "inbreeding":
gwas_object._output_statistics(inbreeding=options.sum_param)
elif options.summary_method == "inbreeding_coef":
gwas_object._output_statistics(inbreeding_coef=options.sum_param)
elif options.summary_method == "gender_checker":
gwas_object._output_statistics(gender_checker=options.sum_param)
elif options.summary_method == "wrights_fst":
gwas_object._output_statistics(wrights_fst=options.sum_param)
else:
pass
elif options.method == "remove_relations":
gwas_object._run_tasks(remove_relations="cutoff",
parameter=options.threshold)
elif options.method == "check_gender":
gwas_object._run_tasks(check_gender="")
else:
pass
gwas_object.build_statement(infiles=geno_files,
outfile=options.out_pattern,
threads=options.threads,
memory=options.memory,
parallel=options.parallel)
# write footer and output benchmark information.
E.Stop()