From e8997bdaca4abdd92169baeb151ca9fcd67f9e5f Mon Sep 17 00:00:00 2001
From: Nathan Lecouvreur <nathan.lecouvreur@ens-lyon.fr>
Date: Wed, 2 Feb 2022 10:49:30 +0100
Subject: [PATCH] made finder runnable
---
GATC_finder.py | 35 +++++++++++++++++++++++++++++++++++
src/GATC_analysis.py | 8 +++++++-
src/GATC_finder.py | 39 ++++++++++++++++++++++-----------------
3 files changed, 64 insertions(+), 18 deletions(-)
create mode 100644 GATC_finder.py
diff --git a/GATC_finder.py b/GATC_finder.py
new file mode 100644
index 0000000..a14cbf6
--- /dev/null
+++ b/GATC_finder.py
@@ -0,0 +1,35 @@
+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/GATC_analysis.py b/src/GATC_analysis.py
index 5d837c2..1a75638 100644
--- a/src/GATC_analysis.py
+++ b/src/GATC_analysis.py
@@ -69,9 +69,15 @@ for chrom, regions, name in zip(chromosomes, chrom_regions, id_list):
if j >= 5:
j = 0
i += 1
-
+
+ pos = np.arange(1, int(max(regions)), 1 )
+ y = np.full(len(pos), 39)
+ print(len(pos))
+ print(len(y))
+
axes[i, j].set_title(name)
axes[i, j].set_ylabel("site number / bin")
+ axes[i, j].plot(pos, y, color = "black")
axes[i, j].plot(regions, chrom)
j += 1
diff --git a/src/GATC_finder.py b/src/GATC_finder.py
index 12816e8..a14cbf6 100644
--- a/src/GATC_finder.py
+++ b/src/GATC_finder.py
@@ -1,30 +1,35 @@
import re
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas
-from Bio import SeqIO, motifs
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
+from Bio import SeqIO
-def main():
+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")
- f = open("/home/nathan/projects/vscode_nextflow/nextflow-nathan/results/GATC/sites.bed", "w")
motif = "GATC"
- pos_list = list()
-
- for seq_record in SeqIO.parse("/home/nathan/projects/vscode_nextflow/nextflow-nathan/data/genome/data_G.fasta", "fasta"):
- chrom = seq_record.id
+
+ # 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
-
- line = f"{chrom}\t{start_pos}\t{end_pos}\n"
-
- f.write(line)
+ # 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()
\ No newline at end of file
+ main()
--
GitLab