From 094afed7c72448c0382b5c0236c4c26510086bf7 Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Tue, 30 Jun 2020 09:09:12 +0200
Subject: [PATCH] blastn spacers crispr
---
global.smk | 1 +
virome.smk | 28 ++++++++++++++++++++++++++++
2 files changed, 29 insertions(+)
diff --git a/global.smk b/global.smk
index 4aea719..5cf1cc5 100644
--- a/global.smk
+++ b/global.smk
@@ -29,6 +29,7 @@ rule all:
#virome
expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
expand("work/virhostmatcher/{sample}/done", sample=config["SAMPLES"]),
+ expand("work/blast/spacer_{sample}.tsv", sample=config["SAMPLES"]),
include: "../workflow_metagenomics/quality.smk"
diff --git a/virome.smk b/virome.smk
index 42f2a70..e78abfb 100644
--- a/virome.smk
+++ b/virome.smk
@@ -45,3 +45,31 @@ rule virhostmatcher:
# "conda deactivate "
"&& "
"touch {output.done} "
+
+rule crispr:
+ input:
+ unpack(contigs_input)
+ output:
+ "work/blast/{db}_{sample}.tsv"
+ params:
+ db = "DATA/blast/{db}", # wget https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=20190618_spacer_34.zip -O DATA/spacer.zip && unzip DATA/spacer.zip -d DATA && rm DATA/spacer.zip && makeblastdb -in DATA/20190618_spacer_34.fasta -dbtype nucl -out DATA/blast/spacer && rm DATA/20190618_spacer_34.fasta
+ header = "qaccver qlen qseq saccver slen sseq pident mismatch gapopen evalue bitscore qcovs length qstart qend sstart send"
+ threads:
+ 20
+ shell:
+ "conda activate blast-2.9.0 "
+ "&& "
+ "blastn "
+ "-task blastn-short "
+ "-db {params.db} "
+ "-query {input} "
+ "-out {output} "
+ "-outfmt '6 {params.header}' "
+ "-evalue 0.003 "
+ "-word_size 6 "
+ "-gapopen 10 "
+ "-gapextend 2 "
+ "-penalty -1 "
+ "-max_target_seqs 1000 "
+ "&& "
+ "conda deactivate "
--
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