This repository contains the program to compute the similarity matrix of k-mer counts vectors for a list of datasets, and also contains the programs to perform the seeded-chunking and to compute the Hausdorff distances used in the Hierarchical Representative Set Selection. The Hierarchical Representative Set Selection can be found in this repository: https://github.com/Kingsford-Group/hierrepsetselection
Download the source code from this repository. And then use the following commands to compile:
autoreconf -fi
./configure
make
This program can be used for any applications. The cosine similarity is the similarity measure. Use the following command to get the similarity matrix of k-mer counts vectors for a list of datasets:
sortsim <klen> <list_datasets_file>
where <klen> is the k-mer size (e.g. 17), and <list_datasets_file> is a file containing the names of all the datasets' k-mer counts files (full-path), one filename per line. Note that these k-mer counts files are gzipped.
The seeded-chunking method produces chunks as separately as possible from the original set of datasets. Use the following command to perform the seeded-chunking:
chunking <klen> <full_set_datasets_file> <rand_set_datasets_file> <num_chunks> <chunk_size>
where <klen> is the k-mer size (e.g. 17), <full_set_datasets_file> is a file containing the names of all the datasets' k-mer counts files (full-path) in the original full set to be chunked (one filename per line), <rand_set_datasets_file> is a file containing the names of randomly selected datasets' k-mer counts files (these datasets are selected randomly from the original full set and will be used for selecting seeds), <num_chunks> is the number of chunks, and <chunk_size> is the size of each chunk. All these these k-mer counts files are gzipped.
Both the classical Hausdorff distance and the partial Hausdorff distance are computed. Use the following command to compute the Hausdorff distances:
hausdorff <klen> <full_set_datasets_file> <rep_set_datasets_file> <q>
where <klen> is the k-mer size (e.g. 17), <full_set_datasets_file> is a file containing the names of all the datasets' k-mer counts files (full-path) in the original full set, <rep_set_datasets_file> is a file containing the names of the selected representative datasets' k-mer counts files, and <q> is a parameter used in the partial Hausdorff distance: q = 1 – K / |X| where |X| is the size of the original full set, and K is for using the Kth largest value (counting from the minimum) as the partial Hausdorff distance. All these k-mer counts files are gzipped.