prism.util module

class prism.util.Region

Bases: prism.util.Region

prism.util.extract_chromosome(header)

Extract chromosome information for epilocus header.

prism.util.get_bam_handle(bam_path)

Returns pysam.AlignmentFile object for BAM file.

prism.util.get_binary_string_representation(read)

Returns a binary representation string of methylation state of a read. Unmethylated state = 0, methylated state = 1.

prism.util.get_common_headers_by_jaccard_similarity(headers1, headers2, cutoff=0.5)

Given two lists of epiloci headers, determine which epiloci are common.

prism.util.is_fully_methylated_or_unmethylated(pattern)

prism.util.jaccard_similarity(s1, s2)

Compute Jaccard similarity of two sets.

prism.util.merge_two_headers(h1, h2)

Union two epiloci headers.

prism.util.parse_result_line(line)

Parse each line in the PRISM result file.

prism.util.pattern_counters_from_met(fp)

Parse MET file and generate header, and counter of patterns.

prism.util.prepare_header_bed(headers)

Converts a list of epiloci headers to a BedTool object.

prism.util.preset_rc(scale=1, font_family=None)

Set visually plausible matplotlib rc file.

prism.util.random_pattern(l, n)

Generate n random methylation pattern with length l.