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ALLCools._allc_to_bigwig_new

ALLCools._allc_to_bigwig_new

Module Contents

class ContextCounter(mc_contexts)[source]
add(self, context, mc, cov)[source]
class StrandContextCounter(mc_contexts)[source]
add(self, context, strand, mc, cov)[source]
write_entry(counter, context_handle, mc_contexts, strandness, chrom, bin_start, bin_size)[source]
allc_to_bigwig(allc_path, output_prefix, bin_size, mc_contexts, chrom_size_path, strandness)[source]

Generate BigWig files from one ALLC file.

Parameters

  • allc_path – {allc_path_doc}

  • output_prefix – Path prefix of the output BigWig file.

  • bin_size – {bw_bin_sizes_doc}

  • mc_contexts – {mc_contexts_doc}

  • strandness – {strandness_doc}

  • chrom_size_path – {chrom_size_path_doc} If chrom_size_path provided, will use it to extract ALLC with chrom order, but if region provided, will ignore this.

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