diff --git a/data/v1.3/Graphs/MHC-CHM13.0.gfa.gz b/data/v1.3/Graphs/MHC-CHM13.0.gfa.gz deleted file mode 100644 index 7db966d..0000000 Binary files a/data/v1.3/Graphs/MHC-CHM13.0.gfa.gz and /dev/null differ 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 deleted file mode 100644 index 86b4df2..0000000 Binary files a/data/v1.3/Reads/MHC_CHM13_ONT_filt.part_001.fq.gz and /dev/null differ 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 deleted file mode 100644 index f88aefb..0000000 Binary files a/data/v1.3/Reads/MHC_CHM13_ONT_filt.part_002.fq.gz and /dev/null differ diff --git a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.fq.gz b/data/v1.3/Reads/MHC_CHM13_PacBio_filt.fq.gz deleted file mode 100644 index 96dfe5e..0000000 Binary files a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.fq.gz and /dev/null differ 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 deleted file mode 100644 index e16b448..0000000 Binary files a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.part_001.fq.gz and /dev/null differ 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 deleted file mode 100644 index d332a50..0000000 Binary files a/data/v1.3/Reads/MHC_CHM13_PacBio_filt.part_002.fq.gz and /dev/null differ diff --git a/data/v1.3/Reproduce.py b/data/v1.3/Reproduce.py index 48a3af5..518fd92 100755 --- 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