ALLCools._doc

Module Contents

idx_doc = If true, save an methylpy chromosome index for back compatibility. If you only use methylpy to...[source]
allc_path_doc = Path to 1 ALLC file[source]
allc_paths_doc = Single ALLC path contain wildcard OR multiple space separated ALLC paths OR a file contains 1...[source]
allc_table_doc = Contain all the ALLC file information in two tab-separated columns: 1. file_uid, 2. file_path. No header[source]
binarize_doc = If set, binarize each single site in each individual ALLC file. This means each cytosine will...[source]
bin_sizes_doc = Fix-size genomic bins can be defined by bin_sizes and chrom_size_path. Space separated sizes of...[source]
bw_bin_sizes_doc = Bin size of the BigWig files.[source]
chrom_size_path_doc = Path to UCSC chrom size file. This can be generated from the genome fasta or downloaded via UCSC...[source]
compress_level_doc = Compression level for the output file[source]
cov_cutoff_doc = Max cov filter for a single site in ALLC. Sites with cov > cov_cutoff will be skipped.[source]
cpu_basic_doc = Number of processes to use in parallel.[source]
mc_contexts_doc = Space separated mC context patterns to extract from ALLC. The context length should be the same...[source]
mc_context_mcad_doc = mC context pattern to extract from ALLC. Context pattern follows IUPAC nucleotide code, e.g. N...[source]
reference_fasta_doc = Path to 1 genome reference FASTA file (the one used for mapping), use samtools fadix to build...[source]
region_bed_names_doc = Space separated names for each BED file provided in region_bed_paths.[source]
region_bed_paths_doc = Arbitrary genomic regions can be defined in several BED files to count on. Space separated paths...[source]
region_bed_path_mcad_doc = Arbitrary genomic regions can be defined in one BED file to count on. The fourth column of the...[source]
region_doc = Only extract records from certain genome region(s) via tabix, multiple region can be provided in...[source]
remove_additional_chrom_doc = Whether to remove rows with unknown chromosome instead of raising KeyError[source]
rna_table_doc = This is only for mCT data when we have RNA BAM file for each single cell. Contain all the RNA...[source]
snp_doc = If true, means the input allc contain snp information, and the allc processing will take care that.[source]
split_strand_doc = If true, Watson (+) and Crick (-) strands will be count separately[source]
strandness_doc = What to do with strand information, possible values are: 1. both: save +/- strand together in...[source]
generate_dataset_doc = Generate MCDS dataset from a list of ALLC files (recorded in the allc_table). Multiple region...[source]
generate_dataset_obs_dim_doc = Name of the observation dimension.[source]
generate_dataset_chunk_size_doc = Chunk allc_table with chunk_size when generate dataset in parallel[source]
generate_dataset_regions_doc = Definition of genomic regions in the form of "--regions {region_name} {region_definition}". This...[source]
generate_dataset_quantifiers_doc = Definition of genome region quantifiers in the form of "--quantifiers {region_name} {quant_type}...[source]
table_to_allc_doc = Convert different kinds of methylation table into ALLC format. Currently, only plain text table...[source]
table_to_allc_input_path = input path of the table[source]
table_to_allc_output_prefix = output prefix of the ALLC table[source]
table_to_allc_sep = character to separate columns in the table[source]
table_to_allc_header = Whether the table contains header line or not[source]
table_to_allc_chunk_size = chunk_size to perform conversion[source]
table_to_allc_chrom = the chromosome column number, 0-based index[source]
table_to_allc_pos = the position column number, 0-based index[source]
table_to_allc_strand = the strand column number, 0-based index. If not provided, will infer automatically based on the...[source]
table_to_allc_context = the cytosine context column number, 0-based index. If not provided, will inter automatically...[source]
table_to_allc_mc = the methylated cytosine count column number, 0-based index.[source]
table_to_allc_uc = the unmethylated cytosine count column number, 0-based index.[source]
table_to_allc_cov = the total cytosine coverage count column number, 0-based index.[source]
table_to_allc_mc_frac = the methylation fraction column number, 0-based index.[source]
table_to_allc_pseudo_count = Use this pseudo_count number as the total cytosine coverage count, if the "cov" column is...[source]
table_to_allc_fasta_path = the genome FASTA file path, required if either "strand" or "context" column is missing.[source]
table_to_allc_num_upstream_bases = number of up stream bases to include when get cytosine context.[source]
table_to_allc_num_downstream_bases = number of down stream bases to include when get cytosine context.[source]
table_to_allc_add_chr = whether add "chr" before the chromosome name.[source]
table_to_allc_sort = whether sort the ALLC table after conversion.[source]
doc_params(**kwds)[source]

Docstrings should start with “” in the first line for proper formatting.