added zenodo link for datasets

at-cg · Feb 15, 2024 · 781a944 · 781a944
1 parent 865979a
commit 781a944
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Showing 7 changed files with 23 additions and 2 deletions.
diff --git a/data/v1.3/Graphs/MHC-CHM13.0.gfa.gz b/data/v1.3/Graphs/MHC-CHM13.0.gfa.gz
diff --git a/data/v1.3/Reads/MHC_CHM13_ONT_filt.part_001.fq.gz b/data/v1.3/Reads/MHC_CHM13_ONT_filt.part_001.fq.gz
diff --git a/data/v1.3/Reads/MHC_CHM13_ONT_filt.part_002.fq.gz b/data/v1.3/Reads/MHC_CHM13_ONT_filt.part_002.fq.gz
diff --git a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.fq.gz b/data/v1.3/Reads/MHC_CHM13_PacBio_filt.fq.gz
diff --git a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.part_001.fq.gz b/data/v1.3/Reads/MHC_CHM13_PacBio_filt.part_001.fq.gz
diff --git a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.part_002.fq.gz b/data/v1.3/Reads/MHC_CHM13_PacBio_filt.part_002.fq.gz
diff --git a/data/v1.3/Reproduce.py b/data/v1.3/Reproduce.py
@@ -86,9 +86,30 @@
 
 map_threads = 6
 # Generate the graph
-os.system("python3 Gen_Graph.py -t " + str(threads))
+# os.system("python3 Gen_Graph.py -t " + str(threads))
 # Simulate queries
-os.system("source ~/.bashrc && conda activate MC && python3 Simulate_query.py -t " + str(threads))
+# os.system("source ~/.bashrc && conda activate MC && python3 Simulate_query.py -t " + str(threads))
+
+os.system("mkdir -p Graphs")
+os.system("mkdir -p Reads")
+os.system("curl https://zenodo.org/api/records/10665350/files-archive -o Data.zip")
+os.system("unzip Data.zip")
+os.system("mv *.gfa.gz Graphs/")
+os.system("mv *.fq.gz Reads/")
+os.system("rm -rf Query_0.1")
+os.system("rm -rf Query_1")
+os.system("rm -rf Query_5")
+os.system("tar -xvf Query_0.1.tar.gz")
+os.system("tar -xvf Query_1.tar.gz")
+os.system("tar -xvf Query_5.tar.gz")
+os.system("cd Query_0.1 && gunzip *")
+os.system("cd Query_1 && gunzip *")
+os.system("cd Query_5 && gunzip *")
+os.system("rm Query_0.1.tar.gz")
+os.system("rm Query_1.tar.gz")
+os.system("rm Query_5.tar.gz")
+os.system("echo $(pwd)")
+
 # Map the queries
 os.system("source ~/.bashrc && conda activate MC && python3 Map_Graph.py -t " + str(threads))
 # Map the reads