Skip to content
Snippets Groups Projects
Commit 5c61a425 authored by Lihouck Flavien's avatar Lihouck Flavien
Browse files

Output changed for Snakefile

parent 948cadf0
Branches
No related tags found
No related merge requests found
DATASET = "../../data/msa"
DATA = "../../data"
DATASET = expand("{data}/msa", data=DATA)
TOOL = ["abpoa", "kalign", "kalign3", "mafft", "muscle", "spoa"]
THRESHOLD = ["50", "60", "70", "80", "90"]
REGION = ["100", "200", "500", "1000", "2000"]
......@@ -6,7 +7,7 @@ DEPTH = ["10", "20", "50", "100", "150"]
ALIGN = ["muscle", "mafft"]
rule all:
input: expand("consensus/{region}/{depth}/aln_all_consensus.txt", region=REGION, depth=DEPTH)
input: expand("consensus/aln_all_consensus_r{region}_d{depth}.txt", region=REGION, depth=DEPTH)
rule MTool:
......@@ -35,8 +36,8 @@ rule final_consensus:
shell: "./msa_handler/MTool consensus/{wildcards.region}/{wildcards.depth}/{wildcards.align}_consensus_{wildcards.region}_{wildcards.depth}_{wildcards.threshold}.fasta consensus/{wildcards.region}/{wildcards.depth}/{wildcards.align}_final_consensus_{wildcards.region}_{wildcards.depth}_{wildcards.threshold}.fasta {wildcards.threshold} 2"
rule exonerate_ref_result:
input: files=expand("consensus/{region}/{depth}/muscle_final_consensus_{region}_{depth}_{threshold}.fasta", threshold=THRESHOLD, allow_missing=True) , ref="../data/seq_selectes_region/region_seq_r{region}.fasta"
input: files=expand("consensus/{region}/{depth}/muscle_final_consensus_{region}_{depth}_{threshold}.fasta", threshold=THRESHOLD, allow_missing=True) , ref=expand("{data}/seq_selectes_region/region_seq_r{region}.fasta", data=DATA, allow_missing=True)
output: "consensus/aln_all_consensus_r{region}_d{depth}.txt"
conda: "envs/exonerate.yaml"
shell: "for FILE in {input.files}; do exonerate --bestn 1 -Q dna -E -m a:g {input.ref} $FILE >> {output}; done"
shell: "for FILE in {input.files}; do exonerate --bestn 1 -Q dna -E -m a:g {input.ref} $FILE >> {output}; done 2>/dev/null"
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment