Commit 03b526bc authored by Laura Denies's avatar Laura Denies
Browse files

update HMM virulence prediction report

parent 850f0c34
...@@ -2,7 +2,7 @@ pathofact: ...@@ -2,7 +2,7 @@ pathofact:
sample: ["test_sample"] # requires user input sample: ["test_sample"] # requires user input
project: PathoFact_update_trial # requires user input project: PathoFact_update_trial # requires user input
datadir: ../test_dataset # requires user input datadir: ../test_dataset # requires user input
workflow: "Tox" workflow: "Vir"
size_fasta: 1000 size_fasta: 1000
scripts: "scripts" scripts: "scripts"
signalp: "/work/projects/ecosystem_biology/local_tools/SignalP/signalp-5.0b/bin" # requires user input signalp: "/work/projects/ecosystem_biology/local_tools/SignalP/signalp-5.0b/bin" # requires user input
......
...@@ -10,7 +10,7 @@ import os ...@@ -10,7 +10,7 @@ import os
rule merge_SignalPVir: rule merge_SignalPVir:
input: input:
Vir="{datadir}/{project}/VIRULENCE/HMM_classifier_virulence/{sample}_virulence_final_prediction.tsv", Vir="{datadir}/{project}/VIRULENCE/HMM_classifier_virulence/{sample}_virulence_final_prediction.tsv",
SignalP="{datadir}/{project}/SignalP/aggregated/{sample}_SignalP_results.txt" SignalP="{datadir}/{project}/SignalP/aggregated/{sample}_SignalP_results.tsv"
output: output:
"{datadir}/{project}/VIRULENCE/virulence_merged/{sample}_virulence_SignalP_prediction.tsv" "{datadir}/{project}/VIRULENCE/virulence_merged/{sample}_virulence_SignalP_prediction.tsv"
params: params:
......
...@@ -88,44 +88,23 @@ rule HMM_R_VIR: ...@@ -88,44 +88,23 @@ rule HMM_R_VIR:
"../../scripts/hmm.R" "../../scripts/hmm.R"
# Give pathogenicity prediction # Give pathogenicity prediction
rule HMM_VIR_nonpath: rule HMM_VIR_classification:
input: input:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv" "{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv"
output: output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_non_path.txt") non_path=temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_non_path.txt"),
pathogenic=temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_pathogenic.txt"),
unclassified=temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_unclassified.txt")
params: params:
runtime=config["pathofact"]["runtime"]["short"], runtime=config["pathofact"]["runtime"]["short"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"] mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
shell: shell:
""" """
awk '$2 == "True" && $3 == "False" && $4 == "False"' {input} | awk '$5 = "Non-Pathogenic"' | sed 's/ /\\t/g' > {output} awk '$2 == "True" && $3 == "False" && $4 == "False"' {input} | awk '$5 = "Non-Pathogenic"' | sed 's/ /\\t/g' > {output.non_path}
awk '$3 == "True"' {input} | awk '$5 = "Pathogenic"' | sed 's/ /\\t/g' > {output.pathogenic}
awk '$3 == "False" && $4 == "True"' {input} | awk '$5 = "Unclassified"' | sed 's/ /\\t/g' > {output.unclassified}
""" """
rule HMM_VIR_pathogenic:
input:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv"
output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_pathogenic.txt")
params:
runtime=config["pathofact"]["runtime"]["short"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
shell:
"""
awk '$3 == "True"' {input} | awk '$5 = "Pathogenic"' | sed 's/ /\\t/g' > {output}
"""
rule HMM_VIR_unclassified:
input:
"{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}.hmm_results.csv"
output:
temp("{datadir}/{project}/VIRULENCE/HMM_virulence/{sample}_hmm_unclassified.txt")
params:
runtime=config["pathofact"]["runtime"]["short"],
mem=config["pathofact"]["mem"]["normal_mem_per_core_gb"]
shell:
"""
awk '$3 == "False" && $4 == "True"' {input} | awk '$5 = "Unclassified"' | sed 's/ /\\t/g' > {output}
"""
rule HMM_VIR_report: rule HMM_VIR_report:
input: input:
......
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