Contents

ALLCools.table_to_allc

ALLCools.table_to_allc

Module Contents

mode_mc_cov(table, mc, cov)[source]
mode_mc_uc(table, mc, uc)[source]
mode_uc_cov(table, uc, cov)[source]
mode_mc_frac_cov(table, mc_frac, cov)[source]
mode_mc_frac_mc(table, mc_frac, mc)[source]
mode_mc_frac_uc(table, mc_frac, uc)[source]
mode_mc_frac_pseudo_count(table, mc_frac, pseudo_count)[source]
get_strand(chrom, pos, fasta)[source]
get_context(chrom, pos, strand, fasta, num_upstream_bases, num_downstream_bases)[source]
get_strand_and_context(table, chrom, pos, strand, context, fasta_path, num_upstream_bases, num_downstream_bases)[source]
dataframe_to_allc(table, add_chr=False, chrom=0, pos=1, strand=None, context=None, fasta_path=None, chrom_sizes=None, mc=None, uc=None, cov=None, mc_frac=None, pseudo_count=1, num_upstream_bases=0, num_downstream_bases=2)[source]
table_to_allc(input_path, output_prefix, sep='\t', header=None, chunk_size=100000, chrom=0, pos=1, strand=None, context=None, mc=None, uc=None, cov=None, mc_frac=None, pseudo_count=1, fasta_path=None, num_upstream_bases=0, num_downstream_bases=2, add_chr=False, sort=True)[source]

{table_to_allc_doc}

Parameters

  • input_path – {table_to_allc_input_path}

  • output_prefix – {table_to_allc_output_prefix}

  • sep – {table_to_allc_sep}

  • header – {table_to_allc_header}

  • chunk_size – {table_to_allc_chunk_size}

  • chrom – {table_to_allc_chrom}

  • pos – {table_to_allc_pos}

  • strand – {table_to_allc_strand}

  • context – {table_to_allc_context}

  • mc – {table_to_allc_mc}

  • uc – {table_to_allc_uc}

  • cov – {table_to_allc_cov}

  • mc_frac – {table_to_allc_mc_frac}

  • pseudo_count – {table_to_allc_pseudo_count}

  • fasta_path – {table_to_allc_fasta_path}

  • num_upstream_bases – {table_to_allc_num_upstream_bases}

  • num_downstream_bases – {table_to_allc_num_downstream_bases}

  • add_chr – {table_to_allc_add_chr}

  • sort – {table_to_allc_sort}

Returns

Return type

output path of the converted ALLC file.

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