From 355fc1feca9852de072700ab74a0df0e39265433 Mon Sep 17 00:00:00 2001
From: Iris Mestres <iris.mestrespascual@unibas.ch>
Date: Mon, 20 Feb 2023 12:26:56 +0100
Subject: [PATCH] Add rule to sort isomiRs annotation file
---
workflow/rules/quantify.smk | 192 ++++++++++++++++++++++++------------
1 file changed, 129 insertions(+), 63 deletions(-)
diff --git a/workflow/rules/quantify.smk b/workflow/rules/quantify.smk
index 90fd572..292ffa2 100644
--- a/workflow/rules/quantify.smk
+++ b/workflow/rules/quantify.smk
@@ -8,7 +8,6 @@
# USAGE (from the file's directory):
#
# snakemake \
-# --snakefile="quanitfy.smk" \
# --cores 4 \
# --use-singularity \
# --singularity-args "--bind $PWD/../" \
@@ -16,9 +15,6 @@
# --rerun-incomplete \
# --verbose
#
-# IMPORTANT when executing this file alone:
-## * You must modify the config.yaml.
-## * Uncomment the configfile line.
################################################################################
import os
@@ -133,6 +129,72 @@ rule sort_alignments:
) &> {log}"
+###############################################################################
+### Sort isomiRs
+###############################################################################
+
+
+rule sort_isomirs:
+ input:
+ isomirs=config["isomirs_anno"],
+ output:
+ isomir=os.path.join(
+ config["output_dir"], "sorted_isomirs.bed"
+ ),
+ params:
+ cluster_log=os.path.join(
+ config["cluster_log"], "sortisomirs.log"
+ ),
+ log:
+ os.path.join(config["local_log"], "sortisomirs.log"),
+ resources:
+ mem=4,
+ threads=8,
+ singularity:
+ "docker://zavolab/ubuntu:18.04"
+ shell:
+ "(sort \
+ -k1,1 \
+ -k2,2n \
+ {input.isomirs} \
+ > {output.isomir} \
+ ) &> {log}"
+
+###############################################################################
+### pre miRNAs intersection
+###############################################################################
+
+
+rule intersect_pre_mirna:
+ input:
+ alignment=os.path.join(
+ config["output_dir"], "{sample}", "sorted.alignments.bed12"
+ ),
+ mirna=config["pre_mirnas_anno"],
+ output:
+ intersect=os.path.join(
+ config["output_dir"], "{sample}", "intersect_pre_mirna.bed"
+ ),
+ params:
+ cluster_log=os.path.join(
+ config["cluster_log"], "intersection_pre_mirna_{sample}.log"
+ ),
+ log:
+ os.path.join(config["local_log"], "intersection_pre_mirna_{sample}.log"),
+ singularity:
+ "docker://zavolab/bedtools:2.27.0"
+ shell:
+ "(bedtools intersect \
+ -wao \
+ -s \
+ -F 1 \
+ -sorted \
+ -b {input.alignment} \
+ -a {input.mirna} \
+ > {output.intersect} \
+ ) &> {log}"
+
+
###############################################################################
### miRNAs intersection
###############################################################################
@@ -161,6 +223,7 @@ rule intersect_mirna:
-wao \
-s \
-F 1 \
+ -f 1 \
-sorted \
-b {input.alignment} \
-a {input.mirna} \
@@ -173,34 +236,37 @@ rule intersect_mirna:
###############################################################################
-# rule intersect_isomirs:
-# input:
-# alignment=os.path.join(
-# config["output_dir"], "{sample}", "sorted.alignments.bed12"
-# ),
-# isomirs=config["isomirs_anno"],
-# output:
-# intersect=os.path.join(
-# config["output_dir"], "{sample}", "intersect_isomirs.bed"
-# ),
-# params:
-# cluster_log=os.path.join(
-# config["cluster_log"], "intersection_isomirs_{sample}.log"
-# ),
-# log:
-# os.path.join(config["local_log"], "intersection_isomirs_{sample}.log"),
-# singularity:
-# "docker://zavolab/bedtools:2.27.0"
-# shell:
-# "(bedtools intersect \
-# -wao \
-# -s \
-# -F 1 \
-# -sorted \
-# -b {input.alignment} \
-# -a {input.isomirs} \
-# > {output.intersect} \
-# ) &> {log}"
+rule intersect_isomirs:
+ input:
+ alignment=os.path.join(
+ config["output_dir"], "{sample}", "sorted.alignments.bed12"
+ ),
+ isomirs=os.path.join(
+ config["output_dir"], "sorted_isomirs.bed"
+ ),
+ output:
+ intersect=os.path.join(
+ config["output_dir"], "{sample}", "intersect_isomirs.bed"
+ ),
+ params:
+ cluster_log=os.path.join(
+ config["cluster_log"], "intersection_isomirs_{sample}.log"
+ ),
+ log:
+ os.path.join(config["local_log"], "intersection_isomirs_{sample}.log"),
+ singularity:
+ "docker://zavolab/bedtools:2.27.0"
+ shell:
+ "(bedtools intersect \
+ -wao \
+ -s \
+ -F 1 \
+ -f 1 \
+ -sorted \
+ -b {input.alignment} \
+ -a {input.isomirs} \
+ > {output.intersect} \
+ ) &> {log}"
###############################################################################
@@ -216,7 +282,7 @@ rule quant_mirna:
script=os.path.join(config["scripts_dir"], "mirna_quantification.py"),
output:
table=os.path.join(
- config["output_dir"], "TABLES", "miRNA_counts_{sample}"
+ config["output_dir"], "TABLES", "miRNA_counts_{sample}"
),
params:
cluster_log=os.path.join(
@@ -246,7 +312,7 @@ rule quant_mirna:
rule quant_mirna_pri:
input:
intersect=os.path.join(
- config["output_dir"], "{sample}", "intersect_mirna.bed"
+ config["output_dir"], "{sample}", "intersect_pre_mirna.bed"
),
script=os.path.join(config["scripts_dir"], "mirna_quantification.py"),
output:
@@ -286,34 +352,34 @@ rule quant_mirna_pri:
###############################################################################
-# rule quant_isomirs:
-# input:
-# intersect=os.path.join(
-# config["output_dir"], "{sample}", "intersect_isomirs.bed"
-# ),
-# script=os.path.join(config["scripts_dir"], "mirna_quantification.py"),
-# output:
-# table=os.path.join(
-# config["output_dir"], "TABLES", "isomirs_counts_{sample}"
-# ),
-# params:
-# cluster_log=os.path.join(
-# config["cluster_log"], "quant_isomirs_{sample}.log"
-# ),
-# prefix=os.path.join(
-# config["output_dir"], "TABLES", "isomirs_counts_{sample}"
-# ),
-# log:
-# os.path.join(config["local_log"], "quant_isomirs_{sample}.log"),
-# singularity:
-# "docker://zavolab/python:3.6.5"
-# shell:
-# "(python \
-# {input.script} \
-# -i {input.intersect} \
-# --uniq=miRNA \
-# -p={params.prefix} \
-# ) &> {log}"
+rule quant_isomirs:
+ input:
+ intersect=os.path.join(
+ config["output_dir"], "{sample}", "intersect_isomirs.bed"
+ ),
+ script=os.path.join(config["scripts_dir"], "mirna_quantification.py"),
+ output:
+ table=os.path.join(
+ config["output_dir"], "TABLES", "isomirs_counts_{sample}"
+ ),
+ params:
+ cluster_log=os.path.join(
+ config["cluster_log"], "quant_isomirs_{sample}.log"
+ ),
+ prefix=os.path.join(
+ config["output_dir"], "TABLES", "isomirs_counts_{sample}"
+ ),
+ log:
+ os.path.join(config["local_log"], "quant_isomirs_{sample}.log"),
+ singularity:
+ "docker://zavolab/python:3.6.5"
+ shell:
+ "(python \
+ {input.script} \
+ -i {input.intersect} \
+ --uniq=miRNA \
+ -p={params.prefix} \
+ ) &> {log}"
###############################################################################
@@ -350,4 +416,4 @@ rule merge_tables:
--output_file {output.table} \
--prefix {params.prefix} \
--verbose \
- ) &> {log}"
\ No newline at end of file
+ ) &> {log}"
--
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