init

partitioning/run_partitions.sh

+#!/bin/bash
+
+
+dir_path=test_10k
+read_number=10000
+# metis params
+cluster_number=30
+cluster_gap=10 # % of size gap between clusters
+
+data_path=$dir_path/data
+
+mkdir $dir_path
+mkdir $data_path
+
+# generate reads, shuffle
+python3 read_matrix.py $data_path $read_number
+
+# test metis :
+# reads_to_graph
+graph_path=$dir_path/reads.graph
+./partitioning $data_path/shuffled_reads.fastq $graph_path --graph
+# run metis
+gpmetis $graph_path $cluster_number -ufactor $cluster_gap > $dir_path/metis.log
+# convert the result file
+metis_output_file=$graph_path".part."$cluster_number
+formated_metis_output=$dir_path"/metis_output.txt"
+python -c "from partitioning import metis_output_to_soluce; metis_output_to_soluce(\"$metis_output_file\", \"$formated_metis_output\")"
+rm $metis_output_file
+
+# test other : read to matrix + run
+./partitioning $data_path/shuffled_reads.fastq $dir_path/matrix.csv --matrix
+
+# eval metis solution
+metis_result=$dir_path/metis_result.txt
+python -c "from partitioning import eval_soluce; eval_soluce(\"$data_path/soluce.txt\",\"$formated_metis_output\", \"$metis_result\")"