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xin-huangxin-huang
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Merge pull request #41 from xin-huang/prefix_removal
remove chr prefix from positive selection rules
2 parents 4361947 + 3e12110 commit 8321bb6

3 files changed

Lines changed: 24 additions & 24 deletions

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‎workflow/rules/4.1_positive_selection_selscan.smk‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -23,10 +23,10 @@ rule extract_snp_pos:
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vcf=rules.polarize_1pop.output.vcf,
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output:
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map=temp(
26-
"results/polarized_data/{species}/{dataset}/1pop/{ppl}/chr{i}.biallelic.snps.map"
26+
"results/polarized_data/{species}/{dataset}/1pop/{ppl}/{i}.biallelic.snps.map"
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),
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log:
29-
"logs/positive_selection/extract_snp_pos.{species}.{dataset}.{ppl}.chr{i}.log",
29+
"logs/positive_selection/extract_snp_pos.{species}.{dataset}.{ppl}.{i}.log",
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conda:
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"../envs/selscape-env.yaml"
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shell:
@@ -42,21 +42,21 @@ rule estimate_selscan_scores:
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map=rules.extract_snp_pos.output.map,
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output:
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out=temp(
45-
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.chr{i}.{method}.out"
45+
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.{i}.{method}.out"
4646
),
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formatted_out=temp(
48-
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.chr{i}.{method}.formatted.out"
48+
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.{i}.{method}.formatted.out"
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),
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log=temp(
51-
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.chr{i}.{method}.log"
51+
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.{i}.{method}.log"
5252
),
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params:
54-
output_prefix="results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.chr{i}",
54+
output_prefix="results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.{i}",
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phasing_flag=get_phasing_flag,
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resources:
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cpus=8,
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log:
59-
"logs/positive_selection/estimate_selscan_scores.{species}.{dataset}.{ppl}.{method}.{maf}.chr{i}.log",
59+
"logs/positive_selection/estimate_selscan_scores.{species}.{dataset}.{ppl}.{method}.{maf}.{i}.log",
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conda:
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"../envs/selscape-env.yaml"
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shell:
@@ -96,7 +96,7 @@ rule merge_selscan_scores:
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done=rules.normalize_selscan_scores.output.done,
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params:
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scores=lambda wc: expand(
99-
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.chr{i}.{method}.formatted.out.100bins.norm",
99+
"results/positive_selection/selscan/{species}/{dataset}/1pop/{ppl}/{method}_{maf}/{ppl}.{i}.{method}.formatted.out.100bins.norm",
100100
i=get_chromosomes(wc),
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species=wc.species,
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dataset=wc.dataset,

‎workflow/rules/4.2_positive_selection_selscan_xp.smk‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -24,22 +24,22 @@ rule extract_pair_snps:
2424
pair_info=rules.create_pair_info.output.pair_info,
2525
output:
2626
vcf1=temp(
27-
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop1.chr{i}.biallelic.snps.vcf.gz"
27+
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop1.{i}.biallelic.snps.vcf.gz"
2828
),
2929
vcf2=temp(
30-
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop2.chr{i}.biallelic.snps.vcf.gz"
30+
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop2.{i}.biallelic.snps.vcf.gz"
3131
),
3232
idx1=temp(
33-
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop1.chr{i}.biallelic.snps.vcf.gz.tbi"
33+
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop1.{i}.biallelic.snps.vcf.gz.tbi"
3434
),
3535
idx2=temp(
36-
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop2.chr{i}.biallelic.snps.vcf.gz.tbi"
36+
"results/polarized_data/{species}/{dataset}/2pop/{pair}/pop2.{i}.biallelic.snps.vcf.gz.tbi"
3737
),
3838
map=temp(
39-
"results/polarized_data/{species}/{dataset}/2pop/{pair}/chr{i}.biallelic.snps.map"
39+
"results/polarized_data/{species}/{dataset}/2pop/{pair}/{i}.biallelic.snps.map"
4040
),
4141
log:
42-
"logs/positive_selection/extract_pair_snps.{species}.{dataset}.{pair}.chr{i}.log",
42+
"logs/positive_selection/extract_pair_snps.{species}.{dataset}.{pair}.{i}.log",
4343
conda:
4444
"../envs/selscape-env.yaml"
4545
shell:
@@ -63,21 +63,21 @@ rule estimate_selscan_xp_scores:
6363
map=rules.extract_pair_snps.output.map,
6464
output:
6565
out=temp(
66-
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.chr{i}.{method}.out"
66+
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.{i}.{method}.out"
6767
),
6868
formatted_out=temp(
69-
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.chr{i}.{method}.formatted.out"
69+
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.{i}.{method}.formatted.out"
7070
),
7171
log=temp(
72-
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.chr{i}.{method}.log"
72+
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.{i}.{method}.log"
7373
),
7474
params:
75-
output_prefix="results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.chr{i}",
75+
output_prefix="results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.{i}",
7676
phasing_flag=get_phasing_flag,
7777
resources:
7878
cpus=8,
7979
log:
80-
"logs/positive_selection/estimate_selscan_xp_scores.{species}.{dataset}.{pair}.{method}.{maf}.chr{i}.log",
80+
"logs/positive_selection/estimate_selscan_xp_scores.{species}.{dataset}.{pair}.{method}.{maf}.{i}.log",
8181
conda:
8282
"../envs/selscape-env.yaml"
8383
shell:
@@ -118,7 +118,7 @@ rule merge_selscan_xp_scores:
118118
done=rules.normalize_selscan_xp_scores.output.done,
119119
params:
120120
scores=lambda wc: expand(
121-
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.chr{i}.{method}.formatted.out.norm",
121+
"results/positive_selection/selscan/{species}/{dataset}/2pop/{pair}/{method}_{maf}/{pair}.{i}.{method}.formatted.out.norm",
122122
i=get_chromosomes(wc),
123123
species=wc.species,
124124
dataset=wc.dataset,

‎workflow/rules/4.3_positive_selection_scikit-allel.smk‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,13 +23,13 @@ rule calc_tajima_d:
2323
vcf=rules.extract_pop_data.output.vcf,
2424
output:
2525
scores=temp(
26-
"results/positive_selection/scikit-allel/{species}/{dataset}/1pop/{ppl}/{method}/{window}_{step}/chr{i}.{method}.scores.txt"
26+
"results/positive_selection/scikit-allel/{species}/{dataset}/1pop/{ppl}/{method}/{window}_{step}/{i}.{method}.scores.txt"
2727
),
2828
params:
2929
window_size="{window}",
3030
step_size_ratio="{step}",
3131
log:
32-
"logs/positive_selection/calc_tajima_d.{species}.{dataset}.{ppl}.{method}.{window}_{step}.chr{i}.log",
32+
"logs/positive_selection/calc_tajima_d.{species}.{dataset}.{ppl}.{method}.{window}_{step}.{i}.log",
3333
conda:
3434
"../envs/selscape-env.yaml"
3535
script:
@@ -41,13 +41,13 @@ rule format_tajima_d:
4141
scores=rules.calc_tajima_d.output.scores,
4242
output:
4343
formatted=temp(
44-
"results/positive_selection/scikit-allel/{species}/{dataset}/1pop/{ppl}/{method}/{window}_{step}/chr{i}.{method}.formatted.txt"
44+
"results/positive_selection/scikit-allel/{species}/{dataset}/1pop/{ppl}/{method}/{window}_{step}/{i}.{method}.formatted.txt"
4545
),
4646
params:
4747
chrom="{i}",
4848
method="{method}",
4949
log:
50-
"logs/positive_selection/format_tajima_d.{species}.{dataset}.{ppl}.{method}.{window}_{step}.chr{i}.log",
50+
"logs/positive_selection/format_tajima_d.{species}.{dataset}.{ppl}.{method}.{window}_{step}.{i}.log",
5151
conda:
5252
"../envs/selscape-env.yaml"
5353
shell:

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