From 89f57db8a659c960a4c6bba052dc338267bf0438 Mon Sep 17 00:00:00 2001
From: Theo <theo.serralta@chu-dijon.fr>
Date: Fri, 20 Oct 2023 15:54:24 +0200
Subject: [PATCH] Creation of a test to read bam with gpu
---
exo_bam_gpu.py | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
create mode 100644 exo_bam_gpu.py
diff --git a/exo_bam_gpu.py b/exo_bam_gpu.py
new file mode 100644
index 0000000..54c5c4b
--- /dev/null
+++ b/exo_bam_gpu.py
@@ -0,0 +1,24 @@
+import pysam
+seq_inf= {}
+
+
+samfile = pysam.AlignmentFile("/home/theo/Documents/alternance/Projet Alternance/dijex8000.bam", "rb")
+for read in samfile.fetch(until_eof=True):
+ seq_id=read.query_name
+ chro=read.reference_name
+ start=read.reference_start
+ lenght=read.query_length
+ end =read.reference_end
+
+ seq_inf[chro]={}
+ seq_inf[chro].append({"seq_id" : seq_id, "start" : start, "end" : end, "lenght" : lenght, })
+
+samfile.close()
+
+def depth_function(data):
+ for chro, data in seq_inf.items():
+ depth = [0] * [-1]["end"] +1 #on crée une liste qui stock la profondeur de chaque chromosome. On prend la dernière position lue de chaque dictionnaire. On rajoute +1 parce que ça compte à partir de 0.
+ for position in range(start, end +1):
+ depth[position] += 1
+depth_function(seq_info)
+
--
2.17.1