From 53c3d377bfc041f30fc8e7e9af911dfe2f4eafcf Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Thu, 5 Sep 2019 12:05:26 +0200
Subject: [PATCH] FragGeneScan prodigal
---
annotation.smk | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++
assembly.smk | 2 +-
config.json | 3 ++-
global.smk | 1 +
4 files changed, 62 insertions(+), 2 deletions(-)
create mode 100644 annotation.smk
diff --git a/annotation.smk b/annotation.smk
new file mode 100644
index 0000000..78b79b7
--- /dev/null
+++ b/annotation.smk
@@ -0,0 +1,58 @@
+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")
+ threads:
+ 4
+ params:
+ output = lambda wildcards, output: os.path.splittext(str(output))[0]
+ shell:
+ "run_FragGeneScan.pl "
+ "-genome={input} "
+ "-out={params.output} "
+ "-complete=0 " #negative values with complete=1
+ "-train=complete "
+ "-thread={threads} "
+ " ; "
+ "sed --in-place 's/*/N/' {output.faa} "
+
+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"
+ shell:
+ "prodigal "
+ "-f gff "
+ "-i {input} "
+ "-a {output.faa} "
+ "-d {output.ffn} "
+ "-o {output.gff} "
+ "-g 11 "
+ "-p meta "
+ # " ; "
+ # "sed --in-place 's/*/N/' {output.faa} "
+
+def faa_input(wildcards):
+ if config["PROTEINS-PREDICTOR"] == "FragGeneScan":
+ return {"faa": "work/FGS/{wildcards.sample}_FGS.faa".format(wildcards=wildcards)}
+ elif config["PROTEINS-PREDICTOR"] == "prodigal":
+ return {"faa": "work/prodigal/{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)}
+ elif config["PROTEINS-PREDICTOR"] == "prodigal":
+ return {"fnn": "work/prodigal/{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)}
+ elif config["PROTEINS-PREDICTOR"] == "prodigal":
+ return {"gff": "work/prodigal/{wildcards.sample}_prodigal.gff".format(wildcards=wildcards)}
diff --git a/assembly.smk b/assembly.smk
index d359f42..879adbd 100644
--- a/assembly.smk
+++ b/assembly.smk
@@ -79,7 +79,7 @@ rule metaspades:
min_len = config["CONTIGS_LEN"],
mem_tot = 250,
input = lambda wildcards, input: " --12 ".join(input),
- output = lambda wildcards, output: os.path.dirname(str(output))
+ output = lambda wildcards, output: os.path.dirname(str(output.contigs))
shell:
"spades.py "
"--threads {threads} "
diff --git a/config.json b/config.json
index c92e0e2..6b7ebc0 100644
--- a/config.json
+++ b/config.json
@@ -3,5 +3,6 @@
"NORMALIZATION": false,
"SORTMERNA": false,
"ASSEMBLER": "metaspades",
- "CONTIGS_LEN": 1000
+ "CONTIGS_LEN": 1000,
+ "PROTEINS-PREDICTOR": "prodigal"
}
diff --git a/global.smk b/global.smk
index dbb749c..e8bd404 100644
--- a/global.smk
+++ b/global.smk
@@ -15,3 +15,4 @@ include: "../workflow_metagenomics/quality.smk"
include: "../workflow_metagenomics/preprocess.smk"
include: "../workflow_metagenomics/kaiju.smk"
include: "../workflow_metagenomics/assembly.smk"
+include: "../workflow_metagenomics/annotation.smk"
--
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