From da39f1fb26d11dfed08a5258c0cb7de29d60912f Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Fri, 6 Sep 2019 17:07:44 +0200
Subject: [PATCH] cdhit catalogue.ffn
---
annotation.smk | 28 ++++++++---------
catalogue.smk | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++
global.smk | 2 ++
3 files changed, 98 insertions(+), 14 deletions(-)
create mode 100644 catalogue.smk
diff --git a/annotation.smk b/annotation.smk
index 0e203c2..c92e44c 100644
--- a/annotation.smk
+++ b/annotation.smk
@@ -2,10 +2,10 @@ rule FragGeneScan:
input:
unpack(contigs_input)
output:
- faa = "work/FGS/{sample}_FGS.faa",
- ffn = "work/FGS/{sample}_FGS.ffn",
- gff = "work/FGS/{sample}_FGS.gff",
- out = temp("work/FGS/{sample}_FGS.out")
+ faa = "work/FGS/{sample}/{sample}_FGS.faa",
+ ffn = "work/FGS/{sample}/{sample}_FGS.ffn",
+ gff = "work/FGS/{sample}/{sample}_FGS.gff",
+ out = temp("work/FGS/{sample}/{sample}_FGS.out")
threads:
4
params:
@@ -24,9 +24,9 @@ rule prodigal:
input:
unpack(contigs_input)
output:
- faa = "work/prodigal/{sample}_prodigal.faa",
- ffn = "work/prodigal/{sample}_prodigal.ffn",
- gff = "work/prodigal/{sample}_prodigal.gff"
+ faa = "work/prodigal/{sample}/{sample}_prodigal.faa",
+ ffn = "work/prodigal/{sample}/{sample}_prodigal.ffn",
+ gff = "work/prodigal/{sample}/{sample}_prodigal.gff"
shell:
"prodigal "
"-f gff "
@@ -41,21 +41,21 @@ rule prodigal:
def faa_input(wildcards):
if config["PROTEINS-PREDICTOR"] == "FragGeneScan":
- return {"faa": "work/FGS/{wildcards.sample}_FGS.faa".format(wildcards=wildcards)}
+ return {"faa": "work/FGS/{wildcards.sample}/{wildcards.sample}_FGS.faa".format(wildcards=wildcards)}
elif config["PROTEINS-PREDICTOR"] == "prodigal":
- return {"faa": "work/prodigal/{wildcards.sample}_prodigal.faa".format(wildcards=wildcards)}
+ return {"faa": "work/prodigal/{wildcards.sample}/{wildcards.sample}_prodigal.faa".format(wildcards=wildcards)}
def ffn_input(wildcards):
if config["PROTEINS-PREDICTOR"] == "FragGeneScan":
- return {"fnn": "work/FGS/{wildcards.sample}_FGS.ffn".format(wildcards=wildcards)}
+ return {"fnn": "work/FGS/{wildcards.sample}/{wildcards.sample}_FGS.ffn".format(wildcards=wildcards)}
elif config["PROTEINS-PREDICTOR"] == "prodigal":
- return {"fnn": "work/prodigal/{wildcards.sample}_prodigal.ffn".format(wildcards=wildcards)}
+ return {"fnn": "work/prodigal/{wildcards.sample}/{wildcards.sample}_prodigal.ffn".format(wildcards=wildcards)}
def gff_input(wildcards):
if config["PROTEINS-PREDICTOR"] == "FragGeneScan":
- return {"gff": "work/FGS/{wildcards.sample}_FGS.gff".format(wildcards=wildcards)}
+ return {"gff": "work/FGS/{wildcards.sample}/{wildcards.sample}_FGS.gff".format(wildcards=wildcards)}
elif config["PROTEINS-PREDICTOR"] == "prodigal":
- return {"gff": "work/prodigal/{wildcards.sample}_prodigal.gff".format(wildcards=wildcards)}
+ return {"gff": "work/prodigal/{wildcards.sample}/{wildcards.sample}_prodigal.gff".format(wildcards=wildcards)}
def db_input(wildcards):
if wildcards.db == "nr":
@@ -156,4 +156,4 @@ rule interproscan:
"--formats tsv,gff3,html "
"--iprlookup "
"--goterms "
- "--pathways "
\ No newline at end of file
+ "--pathways "
diff --git a/catalogue.smk b/catalogue.smk
new file mode 100644
index 0000000..7ff48a1
--- /dev/null
+++ b/catalogue.smk
@@ -0,0 +1,82 @@
+rule partial_genes: #fonctionne uniquement avec prodigal
+ input:
+ "work/prodigal/{sample}/{sample}_prodigal.ffn"
+ output:
+ "work/prodigal/{sample}/{sample}_partial_{x}.ffn"
+ threads:
+ 2
+ shell:
+ "source activate seqkit-0.10.1 "
+ " ; "
+ "seqkit "
+ "grep "
+ "--use-regexp "
+ "--by-name "
+ "--pattern ';partial={wildcards.x};' "
+ "--threads {threads} "
+ "--out-file {output} "
+ "{input} "
+ " ; "
+ "conda deactivate"
+
+rule pool:
+ input:
+ expand("work/prodigal/{sample}/{sample}_partial_{{x}}.ffn", sample=config["SAMPLES"])
+ output:
+ temp("work/prodigal/pool/partial_{x}.ffn")
+ shell:
+ "cat "
+ "{input} "
+ " > "
+ "{output}"
+
+rule pool_incomplet:
+ input:
+ expand("work/cdhit/non_redundant_parial_{x}.ffn", x=["01", "10"])
+ output:
+ temp("work/cdhit/non_redundant_parial_10-01.ffn")
+ shell:
+ "cat "
+ "{input} "
+ " > "
+ "{output}"
+
+rule cd_hit:
+ input:
+ "work/prodigal/pool/partial_{x}.ffn"
+ output:
+ ffn = "work/cdhit/non_redundant_parial_{x}.ffn",
+ clustr = "work/cdhit/non_redundant_parial_{x}.ffn.clustr"
+ threads:
+ 8
+ shell:
+ "cd-hit-est "
+ "-i {input} "
+ "-o {output.ffn} "
+ "-c 0.95 "
+ "-G 1 "
+ "-aS 0.90 "
+ "-d 0 "
+ "-M 0 "
+ "-T {threads} "
+
+rule cd_hit_2D:
+ input:
+ complete = "work/cdhit/non_redundant_parial_00.ffn",
+ incomplete = "work/cdhit/non_redundant_parial_10-01.ffn"
+ output:
+ ffn = "work/cdhit/catalogue.ffn",
+ clustr = "work/cdhit/catalogue.clustr"
+ threads:
+ 8
+ shell:
+ "cd-hit-est-2d "
+ "-i {input.complete} "
+ "-i2 {input.incomplete} "
+ "-o {output.ffn} "
+ "-c 0.95 "
+ "-aS 0.90 "
+ "-g 1 "
+ "-d 0 "
+ "-M 0 "
+ "-T {threads} "
diff --git a/global.smk b/global.smk
index 09b6633..38d01bd 100644
--- a/global.smk
+++ b/global.smk
@@ -16,6 +16,7 @@ rule all:
"report/diamond_nr_coassembly.tsv",
"work/prokka/coassembly_prokka.tsv",
"work/interproscan/coassembly.faa.tsv",
+ "work/cdhit/catalogue.ffn",
include: "../workflow_metagenomics/quality.smk"
@@ -24,3 +25,4 @@ include: "../workflow_metagenomics/kaiju.smk"
include: "../workflow_metagenomics/assembly.smk"
include: "../workflow_metagenomics/annotation.smk"
include: "../workflow_metagenomics/count.smk"
+include: "../workflow_metagenomics/catalogue.smk"
--
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