From 6355ecd1cc1d80dfeeaf364666149efa13fbf7bf Mon Sep 17 00:00:00 2001
From: Nathan Lecouvreur <nathan.lecouvreur@ens-lyon.fr>
Date: Mon, 14 Feb 2022 10:48:45 +0100
Subject: [PATCH] beggining of the implementation
---
src/GATC_analysis.py => GATC_analysis.py | 0
bin_GATC.py | 17 +++++++++
src/.docker_modules/GATC_finder/Dockerfile | 15 ++++++++
.../GATC_finder/script/GATC_finder.py | 32 +++++++++++++++++
src/Dam_ID_analysis.nf | 19 +++++-----
src/GATC_finder.py | 35 -------------------
src/nf_modules/GATC_finder/main.nf | 21 +++++++++++
7 files changed, 94 insertions(+), 45 deletions(-)
rename src/GATC_analysis.py => GATC_analysis.py (100%)
create mode 100644 bin_GATC.py
create mode 100644 src/.docker_modules/GATC_finder/Dockerfile
create mode 100644 src/.docker_modules/GATC_finder/script/GATC_finder.py
delete mode 100644 src/GATC_finder.py
create mode 100644 src/nf_modules/GATC_finder/main.nf
diff --git a/src/GATC_analysis.py b/GATC_analysis.py
similarity index 100%
rename from src/GATC_analysis.py
rename to GATC_analysis.py
diff --git a/bin_GATC.py b/bin_GATC.py
new file mode 100644
index 00000000..c7356eef
--- /dev/null
+++ b/bin_GATC.py
@@ -0,0 +1,17 @@
+import pybedtools
+import pysam
+from Bio import SeqIO
+
+sites = pybedtools.BedTool("/home/nathan/projects/vscode_nextflow/nextflow-nathan/results/GATC/sites_yeast.bed")
+
+
+
+samfile = pysam.AlignmentFile("/home/nathan/projects/vscode_nextflow/nextflow-nathan/results/mapping/data.bam","rb")
+
+print(samfile)
+
+print(samfile)
+for read in samfile.fetch("chr1", 100, 120):
+ print(read)
+
+
diff --git a/src/.docker_modules/GATC_finder/Dockerfile b/src/.docker_modules/GATC_finder/Dockerfile
new file mode 100644
index 00000000..a0265610
--- /dev/null
+++ b/src/.docker_modules/GATC_finder/Dockerfile
@@ -0,0 +1,15 @@
+FROM python:3.8-alpine
+
+RUN apk update \
+ && apk add make automake gcc g++ subversion python3-dev
+
+RUN pip install numpy\
+ && pip install biopython
+
+COPY script/ /script
+
+RUN adduser -D -u 1000 finder
+RUN chown -R finder /script
+USER finder
+
+ENTRYPOINT [ "python","script/GATC_finder.py" ]
\ No newline at end of file
diff --git a/src/.docker_modules/GATC_finder/script/GATC_finder.py b/src/.docker_modules/GATC_finder/script/GATC_finder.py
new file mode 100644
index 00000000..b3e4e037
--- /dev/null
+++ b/src/.docker_modules/GATC_finder/script/GATC_finder.py
@@ -0,0 +1,32 @@
+import sys
+import re
+from Bio import SeqIO
+
+if len(sys.argv) < 3:
+ raise IndexError("Please enter 2 arguments")
+
+# Gets the arguments in the command line
+out_file_path = str(sys.argv[2])
+genome_file = str(sys.argv[1])
+
+# Opening the file to write the positions in
+f = open(out_file_path, "w")
+
+# Motif we are looking for
+motif = "GATC"
+
+# Cycles through the parsed chromosomes from the fasta file
+for seq_record in SeqIO.parse(genome_file, "fasta"):
+
+ # Gets the id of the chormosome in the file
+ chrom = seq_record.id
+
+ # Cycle throught all the motif that are found in the chromosome
+ for match in re.finditer(motif, str(seq_record.seq)):
+
+ start_pos = match.start() +1
+ end_pos = match.end() + 1
+
+ # Writes the position in the .bed file (chro/start/end)
+ line = f"{chrom}\t{start_pos}\t{end_pos}\n"
+ f.write(line)
\ No newline at end of file
diff --git a/src/Dam_ID_analysis.nf b/src/Dam_ID_analysis.nf
index d55f649c..2dd38bf8 100644
--- a/src/Dam_ID_analysis.nf
+++ b/src/Dam_ID_analysis.nf
@@ -4,21 +4,16 @@ nextflow.enable.dsl=2
*/
+include { fastp } from "./nf_modules/fastp/main.nf"
+include { index_fasta ; mapping_fastq } from "./nf_modules/bowtie2/main.nf" addParams(mapping_fastq_out: "mapping/")
-
-
-/*========================= modules import ================================*/
-
-include { fastp } from "./nf_modules/fastp/main.nf"
-
-include { index_fasta; mapping_fastq } from "./nf_modules/bowtie2/main.nf" addParams(mapping_fastq_out: "mapping/")
-
+include { index_bam ; sort_bam} from "./nf_modules/samtools/main.nf"
params.fasta = "data/genome/*_G.fasta"
params.fastq = "data/reads/*_R.fastq"
-
+params.bam = "results/mapping/*.bam"
channel
@@ -32,13 +27,17 @@ channel
.set {fastq_files}
+channel
+ .fromPath(params.bam)
+ .set{bam_file}
/*================================ workflow ================================*/
workflow {
fastp(fastq_files)
- //mapping
index_fasta(fasta_files)
mapping_fastq(index_fasta.out.index.collect(),
fastp.out.fastq)
+ sort_bam(bam_file)
+ index_bam(sort_bam.out.bam)
}
diff --git a/src/GATC_finder.py b/src/GATC_finder.py
deleted file mode 100644
index a14cbf65..00000000
--- a/src/GATC_finder.py
+++ /dev/null
@@ -1,35 +0,0 @@
-import re
-
-from Bio import SeqIO
-
-
-def main(genome_file, out_file_path):
- """[Gets all the GATC file from the given genome or sequence and puts them in a .bed file]
-
- Args:
- genome_file ([string]): [full path to the fasta file]
- out_file_path ([string]): [full path to the output file]
- """
- # Opening the file to write the positions in
- f = open(out_file_path, "w")
-
- motif = "GATC"
-
- # Cycles through the parsed chromosomes from the fasta file
- for seq_record in SeqIO.parse(genome_file, "fasta"):
-
- # Gets the id of the chormosome in the file
- chrom = seq_record.id
-
- # Cycle throught all the motif that are found in the chromosome
- for match in re.finditer(motif, str(seq_record.seq)):
-
- start_pos = match.start() +1
- end_pos = match.end() + 1
-
- # Writes the position in the .bed file (chro/start/end)
- line = f"{chrom}\t{start_pos}\t{end_pos}\n"
- f.write(line)
-
-if __name__ == "__main__":
- main()
diff --git a/src/nf_modules/GATC_finder/main.nf b/src/nf_modules/GATC_finder/main.nf
new file mode 100644
index 00000000..d9c32669
--- /dev/null
+++ b/src/nf_modules/GATC_finder/main.nf
@@ -0,0 +1,21 @@
+container
+
+params.genome = ""
+params.out_file = ""
+
+process GATC_finder {
+ container = "/home/nathan/projects/vscode_nextflow/nextflow-nathan/src/.docker_modules/GATC_finder"
+ label "?"
+ tag "?"
+}
+
+ input:
+ val params.genome
+ val params.out_file
+
+ output:
+ file "sites.bed"
+
+"""
+gatc_finder ${params.genome} ${params.out_file}
+"""
\ No newline at end of file
--
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