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snakefile
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import sys
rule all:
input:
"figures/Figure_1.png",
"figures/Figure_2.png",
"figures/Figure_3.png",
"figures/Figure_4A-B.png",
"figures/Figure_5.png",
"figures/Supp_Figure_1.png",
"figures/Supp_Figure_2.png",
"figures/Supp_Figure_3.png",
"figures/Supp_Figure_4.png",
"figures/Supp_Figure_5.png",
"figures/Supp_Figure_6.png",
"figures/Supp_Figure_7.png",
"figures/Supp_Figure_8.png",
"figures/Supp_Figure_9.png",
"figures/Supp_Figure_10.png",
"figures/Supp_Figure_12.png",
"figures/Figure_1.pdf",
"figures/Figure_2.pdf",
"figures/Figure_3.pdf",
"figures/Figure_4A-B.pdf",
"figures/Figure_5.pdf",
"figures/Supp_Figure_1.pdf",
"figures/Supp_Figure_2.pdf",
"figures/Supp_Figure_3.pdf",
"figures/Supp_Figure_4.pdf",
"figures/Supp_Figure_5.pdf",
"figures/Supp_Figure_6.pdf",
"figures/Supp_Figure_7.pdf",
"figures/Supp_Figure_8.pdf",
"figures/Supp_Figure_9.pdf",
"figures/Supp_Figure_10.pdf",
"figures/Supp_Figure_12.pdf",
"data/stats/Figure_1A_statistics.csv",
"data/stats/Figure_1D_statistics.csv",
"data/stats/Figure_1A_Old_heatmap_stats.csv",
"data/stats/Figure_1A_Young_heatmap_stats.csv",
"data/stats/Figure_1D_Old_heatmap_stats.csv",
"data/stats/Figure_1D_Young_heatmap_stats.csv",
"data/stats/Figure_2_Old_AC_TG_heatmap_stats.csv",
"data/stats/Figure_2_Old_AG_TC_heatmap_stats.csv",
"data/stats/Figure_2_Old_AT_TA_heatmap_stats.csv",
"data/stats/Figure_2_Old_CA_GT_heatmap_stats.csv",
"data/stats/Figure_2_Old_CG_GC_heatmap_stats.csv",
"data/stats/Figure_2_Old_CT_GA_heatmap_stats.csv",
"data/stats/Figure_2_Young_AC_TG_heatmap_stats.csv",
"data/stats/Figure_2_Young_AG_TC_heatmap_stats.csv",
"data/stats/Figure_2_Young_AT_TA_heatmap_stats.csv",
"data/stats/Figure_2_Young_CA_GT_heatmap_stats.csv",
"data/stats/Figure_2_Young_CG_GC_heatmap_stats.csv",
"data/stats/Figure_2_Young_CT_GA_heatmap_stats.csv",
"data/stats/Figure_2_ratio_statistics.csv",
"data/stats/Figure_3A_statistics.csv",
"data/stats/Figure_3B_statistics.csv",
"data/stats/Figure_5_Dunnett_statistics.csv",
"data/stats/Supplemental_Figure_7_statistics.csv",
"data/imported_data/summary_data_wide.csv",
"data/imported_data/summary_data_tidy.csv",
"data/imported_data/mut_file_data.csv",
"data/imported_data/summary_clone_data.csv"
output:
temp(touch(".ruleAllFinished"))
rule initializeEnvs:
input:
"full.initialized"
params:
basePath = sys.path[0]
output:
temp(".env_initialized")
shell:
"""
touch "{output}"
"""
rule initializeFullEnv:
output:
temp("full.initialized")
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
echo "Initializing envs"
touch full.initialized
"""
rule makeDirs:
output:
temp(touch(".dirsMade"))
shell:
"""
mkdir -p data/stats \
data/imported_data \
figures
"""
rule compile_data:
output:
"data/imported_data/summary_data_wide.csv",
"data/imported_data/summary_data_tidy.csv",
"data/imported_data/mut_file_data.csv",
"data/imported_data/summary_clone_data.csv"
priority:
1
shell:
"""
python compile_data.py
"""
rule compute_stats:
input:
"data/imported_data/summary_data_wide.csv",
"data/imported_data/summary_data_tidy.csv",
"data/imported_data/mut_file_data.csv",
"data/imported_data/summary_clone_data.csv",
output:
"data/stats/Figure_1A_statistics.csv",
"data/stats/Figure_1D_statistics.csv",
"data/stats/Figure_1A_Old_heatmap_stats.csv",
"data/stats/Figure_1A_Young_heatmap_stats.csv",
"data/stats/Figure_1D_Old_heatmap_stats.csv",
"data/stats/Figure_1D_Young_heatmap_stats.csv",
"data/stats/Figure_2_Old_AC_TG_heatmap_stats.csv",
"data/stats/Figure_2_Old_AG_TC_heatmap_stats.csv",
"data/stats/Figure_2_Old_AT_TA_heatmap_stats.csv",
"data/stats/Figure_2_Old_CA_GT_heatmap_stats.csv",
"data/stats/Figure_2_Old_CG_GC_heatmap_stats.csv",
"data/stats/Figure_2_Old_CT_GA_heatmap_stats.csv",
"data/stats/Figure_2_Young_AC_TG_heatmap_stats.csv",
"data/stats/Figure_2_Young_AG_TC_heatmap_stats.csv",
"data/stats/Figure_2_Young_AT_TA_heatmap_stats.csv",
"data/stats/Figure_2_Young_CA_GT_heatmap_stats.csv",
"data/stats/Figure_2_Young_CG_GC_heatmap_stats.csv",
"data/stats/Figure_2_Young_CT_GA_heatmap_stats.csv",
"data/stats/Figure_2_ratio_statistics.csv",
"data/stats/Figure_3A_statistics.csv",
"data/stats/Figure_3B_statistics.csv",
"data/stats/Figure_5_Dunnett_statistics.csv",
"data/stats/Supplemental_Figure_7_statistics.csv"
priority:
1
shell:
"""
python compute_stats.py
"""
rule Figure_1:
input:
"data/imported_data/summary_data_wide.csv",
"data/imported_data/summary_data_tidy.csv"
output:
"figures/Figure_1.pdf",
"figures/Figure_1.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Figure_1.py
"""
rule Figure_2:
input:
"data/imported_data/summary_data_wide.csv",
"data/imported_data/summary_data_tidy.csv"
output:
"figures/Figure_2.pdf",
"figures/Figure_2.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Figure_2.py
"""
rule Figure_3:
input:
"data/imported_data/mut_file_data.csv",
"data/imported_data/summary_clone_data.csv"
output:
"figures/Figure_3.pdf",
"figures/Figure_3.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Figure_3.py
"""
rule Figure_4:
input:
"data/imported_data/mut_file_data.csv",
"data/imported_data/summary_clone_data.csv"
output:
"figures/Figure_4A-B.pdf",
"figures/Figure_4A-B.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Figure_4.py
"""
rule Figure_5:
input:
"data/imported_data/summary_data_wide.csv",
"data/imported_data/summary_data_tidy.csv"
output:
"figures/Figure_5.pdf",
"figures/Figure_5.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Figure_5.py
"""
rule Supplemental_Figure_1:
output:
"figures/Supp_Figure_1.pdf",
"figures/Supp_Figure_1.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_1.py
"""
rule Supplemental_Figure_2:
output:
"figures/Supp_Figure_2.pdf",
"figures/Supp_Figure_2.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_2.py
"""
rule Supplemental_Figure_3:
output:
"figures/Supp_Figure_3.pdf",
"figures/Supp_Figure_3.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_3.py
"""
rule Supplemental_Figure_4:
output:
"figures/Supp_Figure_4.pdf",
"figures/Supp_Figure_4.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_4.py
"""
rule Supplemental_Figure_5:
output:
"figures/Supp_Figure_5.pdf",
"figures/Supp_Figure_5.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_5.py
"""
rule Supplemental_Figure_6:
output:
"figures/Supp_Figure_6.pdf",
"figures/Supp_Figure_6.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_6.py
"""
rule Supplemental_Figure_7:
output:
"figures/Supp_Figure_7.pdf",
"figures/Supp_Figure_7.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_7.py
"""
rule Supplemental_Figure_8:
output:
"figures/Supp_Figure_8.pdf",
"figures/Supp_Figure_8.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_8.py
"""
rule Supplemental_Figure_9:
output:
"figures/Supp_Figure_9.pdf",
"figures/Supp_Figure_9.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_9.py
"""
rule Supplemental_Figure_10:
output:
"figures/Supp_Figure_10.pdf",
"figures/Supp_Figure_10.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_10.py
"""
rule Supplemental_Figure_12:
output:
"figures/Supp_Figure_12.pdf",
"figures/Supp_Figure_12.png"
conda:
"Mouse_mtDNA_analysis_env.yaml"
shell:
"""
python3 Supp_Figure_12.py
"""