ALLCools._doc
Contents
ALLCools._doc
¶
Module Contents¶
- idx_doc = If true, save an methylpy chromosome index for back compatibility. If you only use methylpy to...[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]¶
- chrom_size_path_doc = Path to UCSC chrom size file. This can be generated from the genome fasta or downloaded via UCSC...[source]¶
- cov_cutoff_doc = Max cov filter for a single site in ALLC. Sites with cov > cov_cutoff will be skipped.[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]¶
- 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_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_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_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]¶