main module

mavis.cluster.main.main(inputs, output, strand_specific, library, protocol, disease_status, masking, annotations, limit_to_chr=['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y'], cluster_initial_size_limit=25, cluster_radius=100, uninformative_filter=False, max_proximity=5000, min_clusters_per_file=50, max_files=200, batch_id=None, split_only=False, start_time=1558720094, **kwargs)

Parameters:

• inputs (List of str) – list of input files to read
• output (str) – path to the output directory
• strand_specific (bool) – is the bam using a strand specific protocol
• library (str) – the library to look for in each of the input files
• protocol (PROTOCOL) – the sequence protocol (genome or transcriptome)
• masking (object) – see load_masking_regions()
• cluster_clique_size (int) – the maximum size of cliques to search for using the exact algorithm
• cluster_radius (int) – distance (in breakpoint pairs) used in deciding to join bpps in a cluster
• uninformative_filter (bool) – if True then clusters should be filtered out if they are not within a specified (max_proximity) distance to any annotation
• max_proximity (int) – the maximum distance away an annotation can be before the uninformative_filter is applied
• annotations (ReferenceFile) – see load_reference_genes()
• min_clusters_per_file (int) – the minimum number of clusters to output to a file
• max_files (int) – the maximum number of files to split clusters into

mavis.cluster.main.split_clusters(clusters, outputdir, batch_id, min_clusters_per_file=0, max_files=1, write_bed_summary=True)

For a set of clusters creates a bed file representation of all clusters. Also splits the clusters evenly into multiple files based on the user parameters (min_clusters_per_file, max_files)

Returns:of output file names (not including the bed file) Return type:list