structural-constraint-map/Snakefile at main · kumarlab-compomics/structural-constraint-map · GitHub

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import pandas as pd
from glob import glob
import subprocess
import os

#localrules: single_concatenate_summary_metrics, single_concatenate_mtr
#localrules: ensemble_concatenate_summary_metrics, ensemble_concatenate_mtr

localrules: concatenate_cosmis, single_concatenate_summary_metrics, single_concatenate_mtr

if config["run"]["cosmis"] == True and config["run"]["ensemble_structure_modality"] == True and config["run"]["single_structure_modality"] == True:
	rule all:
		input:
			"results/final/all_ensemble_structure_cosmis_scores.csv",
			"results/final/all_single_structure_cosmis_scores.csv"

elif config["run"]["cosmis"] == True and config["run"]["single_structure_modality"] == True:
	rule all:
		input:
			"results/final/all_single_structure_cosmis_scores.csv"

elif config["run"]["single_structure_modality"] == True and config["run"]["ensemble_structure_modality"] == True and config["run"]["cosmis"] == False:
	rule all:
		input:
			"results/single_structure/final/all_transcript_single_structure_summary_metrics.csv",
			"results/single_structure/final/all_single_structure_mtr.csv",
			"results/ensemble_structure/final/all_transcript_ensemble_summary_metrics.csv",
			"results/ensemble_structure/final/all_ensemble_mtr.csv",
			"results/ensemble_structure/final/all_residue_level_ensemble_metrics.csv"

elif config["run"]["single_structure_modality"] == True and config["run"]["ensemble_structure_modality"] == False and config["run"]["cosmis"] == False:
	rule all:
		input:
			"results/single_structure/final/all_transcript_summary_metrics.csv",
			"results/single_structure/final/all_mtr.csv"

elif config["run"]["single_structure_modality"] == False and config["run"]["ensemble_structure_modality"] == True and config["run"]["cosmis"] == False:
	rule all:
		input:
			"results/ensemble_structure/final/all_transcript_ensemble_summary_metrics.csv",
			"results/ensemble_structure/final/all_residue_level_ensemble_metrics.csv",
			"results/ensemble_structure/final/all_ensemble_mtr.csv"

if config["run"]["cosmis"] == True and config["run"]["ensemble_structure_modality"] == True and config["run"]["single_structure_modality"] == True:
	include: "rules/ensemble_structure/utils.smk"
	include: "rules/single_structure/utils.smk"
	include: "rules/ensemble_structure/input_processing.smk"
	include: "rules/ensemble_structure/cosmis.smk"
	include: "rules/single_structure/cosmis.smk"

elif config["run"]["cosmis"] == True and config["run"]["single_structure_modality"] == True:
	include: "rules/single_structure/utils.smk"
	include: "rules/single_structure/cosmis.smk"

elif config["run"]["single_structure_modality"] == True and config["run"]["ensemble_structure_modality"] == True:
	include: "rules/single_structure/utils.smk"
	include: "rules/single_structure/structural_contacts.smk"
        include: "rules/single_structure/community_detection.smk"
        include: "rules/single_structure/mtr.smk"
        include: "rules/single_structure/single_structure_metrics.smk"
	include: "rules/ensemble_structure/utils.smk"
	include: "rules/ensemble_structure/structural_contacts.smk"
        include: "rules/ensemble_structure/community_detection.smk"
        include: "rules/ensemble_structure/mtr.smk"
        include: "rules/ensemble_structure/ensemble_structure_metrics.smk"

elif config["run"]["single_structure_modality"] == True and config["run"]["ensemble_structure_modality"] == False:
	include: "rules/single_structure/utils.smk"
	include: "rules/single_structure/structural_contacts.smk"
	include: "rules/single_structure/community_detection.smk"
	include: "rules/single_structure/mtr.smk"
	include: "rules/single_structure/single_structure_metrics.smk"

elif config["run"]["single_structure_modality"] == False and config["run"]["ensemble_structure_modality"] == True:
	include: "rules/ensemble_structure/utils.smk"
	include: "rules/ensemble_structure/input_processing.smk"
        include: "rules/ensemble_structure/structural_contacts.smk"
        include: "rules/ensemble_structure/community_detection.smk"
        include: "rules/ensemble_structure/mtr.smk"
	include: "rules/ensemble_structure/ensemble_structure_metrics.smk"