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Snakefile
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Snakefile
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configfile: "snake_conf.yaml"
import glob
def get_individuals():
"""read list of sample identifiers"""
if config['samples_file'].endswith(".gz"):
f = gzip.open(config['samples_file'])
else:
f = open(config['samples_file'])
samples = []
for line in f:
samples.append(line.strip())
return samples
rule all:
input:
config['base_dir'] + "/CHT/qqplot.png"
#### Make a QQPlot from CHT results
rule qqplot:
input:
[config['base_dir'] + "/CHT/cht_results.txt",
config['base_dir'] + "/CHT/cht_results_as.txt",
config['base_dir'] + "/CHT/cht_results_bnb.txt",
config['base_dir'] + "/CHT/cht_results_as_permuted.txt",
config['base_dir'] + "/CHT/cht_results_bnb_permuted.txt",
config['base_dir'] + "/CHT/cht_results_permuted.txt"]
output:
config['base_dir'] + "/CHT/qqplot.png"
shell:
"{config[Rscript]} --vanilla "
"{config[wasp_dir]}/CHT/qqplot.R {output[0]} {input}; "
"sleep 10; "
########## Generating HDF5 files for SNPs, genome sequence and read counts
rule snp2h5:
"""Convert impute data files to HDF5 format"""
input:
chrom=config['chrom_info'],
snps=glob.glob(config['snp_dir'] + "/chr*.impute2*gz")
output:
geno_prob=config['base_dir'] + "/snp_h5/geno_probs.h5",
snp_index=config['base_dir'] + "/snp_h5/snp_index.h5",
snp_tab=config['base_dir'] + "/snp_h5/snp_tab.h5",
haplotype=config['base_dir'] + "/snp_h5/haplotype.h5"
shell:
"mkdir -p {config[base_dir]}/snp_h5; "
"{config[wasp_dir]}/snp2h5/snp2h5 --chrom {input.chrom} "
" --format impute "
" --geno_prob {output.geno_prob} "
" --snp_index {output.snp_index} "
" --snp_tab {output.snp_tab} "
" --haplotype {output.haplotype} "
" {input.snps}"
rule fasta2h5:
"""Create HDF5 file from genome FASTA files"""
input:
fasta=glob.glob(config['fasta_dir'] + "/chr*.fa*"),
chrom=config['chrom_info']
output:
config['base_dir'] + "/fasta_h5/seq.h5"
shell:
"mkdir -p {config[base_dir]}/fasta_h5; "
"{config[wasp_dir]}/snp2h5/fasta2h5 --chrom {input.chrom} "
" --seq {output} {input.fasta}"
rule bam2h5:
"""Create HDF5 files of read counts from input BAM files containing
aligned and filtered reads."""
input:
geno_prob=config['base_dir'] + "/snp_h5/geno_probs.h5",
snp_index=config['base_dir'] + "/snp_h5/snp_index.h5",
snp_tab=config['base_dir'] + "/snp_h5/snp_tab.h5",
haplotype=config['base_dir'] + "/snp_h5/haplotype.h5",
snp_samples=config['snp_samples'],
chrom=config['chrom_info'],
bam=lambda wildcards: glob.glob("%s/%s.*%s" % (config['bam_dir'],
wildcards.individual,
config['bam_postfix']))
output:
ref_as=config['base_dir'] + "/bam_h5/ref_as_counts.{individual}.h5",
alt_as=config['base_dir'] + "/bam_h5/alt_as_counts.{individual}.h5",
other_as=config['base_dir'] + "/bam_h5/other_as_counts.{individual}.h5",
read_counts=config['base_dir'] + "/bam_h5/read_counts.{individual}.h5"
shell:
"mkdir -p {config[base_dir]}/bam_h5; "
"{config[py2]} {config[wasp_dir]}/CHT/bam2h5.py --chrom {input.chrom} "
" --snp_index {input.snp_index} "
" --snp_tab {input.snp_tab} "
" --haplotype {input.haplotype} "
" --samples {input.snp_samples} "
" --individual {wildcards.individual} "
" --ref_as_counts {output.ref_as} "
" --alt_as_counts {output.alt_as} "
" --other_as_counts {output.other_as} "
" --read_counts {output.read_counts} "
" {input.bam}"
########### make target regions, extract read counts from them
rule get_target_regions:
"""Extract 'peak' regions that have sufficient read depth
and count of allele specific reads. If different target
regions are desired (e.g. exons), a different script will
need to be used."""
input:
samples=config['samples_file'],
snp_samples=config['snp_samples'],
snp_index=config['base_dir'] + "/snp_h5/snp_index.h5",
snp_tab=config['base_dir'] + "/snp_h5/snp_tab.h5",
haplotype=config['base_dir'] + "/snp_h5/haplotype.h5",
chrom=config['chrom_info'],
ref_as_counts=[config['base_dir'] + "/bam_h5/ref_as_counts.%s.h5" % x
for x in get_individuals()]
output:
config['base_dir'] + "/target_regions.txt.gz"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/get_target_regions.py "
" --target_region_size 2000 "
" --min_as_count {config[min_as_count]} "
" --min_het_count 1 "
" --min_minor_allele_count 1 "
" --chrom {input.chrom} "
" --read_count_dir {config[base_dir]}/bam_h5 "
" --individuals {input.samples} "
" --samples {input.snp_samples} "
" --snp_tab {input.snp_tab} "
" --snp_index {input.snp_index} "
" --haplotype {input.haplotype} "
" --output_file {output}"
rule extract_haplotype_read_counts:
"""Extract haplotype read counts for target regions for each individual."""
input:
snp_samples=config['snp_samples'],
snp_index=config['base_dir'] + "/snp_h5/snp_index.h5",
snp_tab=config['base_dir'] + "/snp_h5/snp_tab.h5",
geno_prob=config['base_dir'] + "/snp_h5/geno_probs.h5",
haplotype=config['base_dir'] + "/snp_h5/haplotype.h5",
samples=config['samples_file'],
chrom=config['chrom_info'],
ref_as_counts=config['base_dir'] + "/bam_h5/ref_as_counts.{individual}.h5",
alt_as_counts=config['base_dir'] + "/bam_h5/alt_as_counts.{individual}.h5",
other_as_counts=config['base_dir'] + "/bam_h5/other_as_counts.{individual}.h5",
read_counts=config['base_dir'] + "/bam_h5/read_counts.{individual}.h5",
target_regions=config['base_dir'] + "/target_regions.txt.gz"
output:
config['base_dir'] + "/hap_read_counts/haplotype_read_counts.{individual}.txt.gz"
shell:
"mkdir -p {config[base_dir]}/hap_read_counts; "
"{config[py2]} {config[wasp_dir]}/CHT/extract_haplotype_read_counts.py "
" --chrom {input.chrom} "
" --snp_index {input.snp_index} "
" --snp_tab {input.snp_tab} "
" --geno_prob {input.geno_prob} "
" --haplotype {input.haplotype} "
" --samples {input.snp_samples} "
" --individual {wildcards.individual} "
" --ref_as_counts {input.ref_as_counts} "
" --alt_as_counts {input.alt_as_counts} "
" --other_as_counts {input.other_as_counts} "
" --read_counts {input.read_counts} "
" {input.target_regions} | gzip > {output}"
########### adjust heterozygote probabilities and read counts
rule make_adj_in_out_files:
"""makes input / output files containing lists of
adjusted read count files"""
input:
["%s/hap_read_counts/haplotype_read_counts.%s.txt.gz" %
(config['base_dir'], x) for x in get_individuals()]
output:
"%s/adjust_hap_read_counts/input.txt" % config['base_dir'],
"%s/adjust_hap_read_counts/output.txt" % config['base_dir']
shell:
"mkdir -p {config[base_dir]}/adjust_hap_read_counts; "
"ls {input} > {output[0]}; "
"ls {input} | sed 's/hap_read_counts/adjust_hap_read_counts/' | "
" sed 's/.txt/.adjusted.txt/' > {output[1]}; "
"sleep 10; "
rule adjust_read_counts:
input:
in_file="%s/adjust_hap_read_counts/input.txt" % config['base_dir'],
out_file="%s/adjust_hap_read_counts/output.txt" % config['base_dir'],
seq=config['base_dir'] + "/fasta_h5/seq.h5"
output:
["%s/adjust_hap_read_counts/haplotype_read_counts.%s.adjusted.txt.gz" %
(config['base_dir'], ind) for ind in get_individuals()]
shell:
"{config[py2]} {config[wasp_dir]}/CHT/update_total_depth.py "
" --seq {input.seq} "
" {input.in_file} {input.out_file}"
rule update_het_probs:
"""adjust heterozygote probabilities in haplotype read count
files"""
input:
hap_read_counts="%s/adjust_hap_read_counts/"
"haplotype_read_counts.{individual}.adjusted.txt.gz" % config['base_dir'],
ref_as_counts="%s/bam_h5/ref_as_counts.{individual}.h5" % config['base_dir'],
alt_as_counts="%s/bam_h5/alt_as_counts.{individual}.h5" % config['base_dir']
output:
"%s/update_het_probs/haplotype_read_counts.{individual}.adjusted.hetp.txt.gz" % \
config['base_dir']
shell:
"mkdir -p {config[base_dir]}/update_het_probs; "
"{config[py2]} {config[wasp_dir]}/CHT/update_het_probs.py "
" --ref_as_counts {input.ref_as_counts} "
" --alt_as_counts {input.alt_as_counts} "
" {input.hap_read_counts} {output}"
rule make_cht_input_files:
"""make the input file containing list of adjusted read count files
that is used for running the combined test"""
input:
expand(config['base_dir'] + "/update_het_probs/haplotype_read_counts."
"{individual}.adjusted.hetp.txt.gz", individual=get_individuals())
output:
"%s/CHT/cht_input_files.txt" % config['base_dir']
shell:
"mkdir -p {config[base_dir]}/CHT; "
"ls {input} > {output}; "
"sleep 10;"
########### Fitting dispersion coefficients for combined test
rule fit_bnb_coef:
"""estimate dispersion parameters for beta-negative binomial
part of combined test"""
input:
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
config['base_dir'] + "/CHT/bnb_coef.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/fit_bnb_coefficients.py "
" --min_as_counts {config[min_as_count]}"
" --sample 2000 --seed 1234 {input.cht_input} {output}"
rule fit_as_coef:
"""estimate dispersion parameters for allele-specific
part of combined test"""
input:
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
config['base_dir'] + "/CHT/as_coef.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/fit_as_coefficients.py "
" {input.cht_input} {output}"
########## Running the combined test on real and permuted data
rule combined_test:
input:
as_coef = config['base_dir'] + "/CHT/as_coef.txt",
bnb_coef = config['base_dir'] + "/CHT/bnb_coef.txt",
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
results = config['base_dir'] + "/CHT/cht_results.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/combined_test.py "
" --min_as_counts {config[min_as_count]}"
" --bnb_disp {input.bnb_coef} --as_disp {input.as_coef}"
" {input.cht_input} {output.results}"
rule as_test:
"""run just the allele-specific part of the combined test"""
input:
as_coef = config['base_dir'] + "/CHT/as_coef.txt",
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
results = config['base_dir'] + "/CHT/cht_results_as.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/combined_test.py"
" --min_as_counts {config[min_as_count]}"
" --as_only --as_disp {input.as_coef}"
" {input.cht_input} {output.results}"
rule bnb_test:
"""run just the beta-negative-binomial part of the combined test"""
input:
bnb_coef = config['base_dir'] + "/CHT/bnb_coef.txt",
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
results = config['base_dir'] + "/CHT/cht_results_bnb.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/combined_test.py "
" --min_as_counts {config[min_as_count]}"
" --bnb_only --bnb_disp {input.bnb_coef}"
" {input.cht_input} {output.results}"
rule as_test_permuted:
"""run just the allele-specific part of the combined test
on permuted genotypes"""
input:
as_coef = config['base_dir'] + "/CHT/as_coef.txt",
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
results = config['base_dir'] + "/CHT/cht_results_as_permuted.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/combined_test.py --shuffle "
" --min_as_counts {config[min_as_count]}"
" --as_only --as_disp {input.as_coef}"
" {input.cht_input} {output.results}"
rule bnb_test_permuted:
"""run just the beta-negative-binomial part of the combined test with
permuted genotypes
"""
input:
bnb_coef = config['base_dir'] + "/CHT/bnb_coef.txt",
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
results = config['base_dir'] + "/CHT/cht_results_bnb_permuted.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/combined_test.py --shuffle"
" --min_as_counts {config[min_as_count]}"
" --bnb_only --bnb_disp {input.bnb_coef}"
" {input.cht_input} {output.results}"
rule combined_test_permuted:
"""Run the combined test on permuted genotypes"""
input:
as_coef = config['base_dir'] + "/CHT/as_coef.txt",
bnb_coef = config['base_dir'] + "/CHT/bnb_coef.txt",
cht_input = config['base_dir'] + "/CHT/cht_input_files.txt"
output:
results = config['base_dir'] + "/CHT/cht_results_permuted.txt"
shell:
"{config[py2]} {config[wasp_dir]}/CHT/combined_test.py --shuffle"
" --min_as_counts {config[min_as_count]}"
" --bnb_disp {input.bnb_coef} --as_disp {input.as_coef}"
" {input.cht_input} {output.results}"