view

View the content of input file (pat/beta) as plain text. For beta files, view as bed. Possible filter by genomic region or sites range Output to stdout as default

Flags:

usage: view [-h] [-s SITES | -r REGION | -L BED_FILE] [--genome GENOME] [--strict] [--strip] [--min_len MIN_LEN] [--shuffle]
            [--no_sort] [--sub_sample SUB_SAMPLE] [-o OUT_PATH] [-np]
            input_file

View the content of input file (pat/beta) as plain text. Possible filter by genomic region or sites range Output to stdout as default

positional arguments:
  input_file

optional arguments:
  -h, --help            show this help message and exit
  -s SITES, --sites SITES
                        a CpG index range, of the form: "450000-450050"
  -r REGION, --region REGION
                        genomic region of the form "chr1:10,000-10,500"
  -L BED_FILE, --bed_file BED_FILE
                        Bed file. Columns <chr, start, end>. For some features columns 4-5 should be <startCpG, endCpG> (run
                        wgbstools convert -L BED_PATH)
  --genome GENOME       Genome reference name. Default is "default".
  --strict              pat: Truncate reads that start/end outside the given region. Only relevant if "region", "sites" or "bed_file"
                        flags are given.
  --strip               pat: Remove trailing dots (from beginning/end of reads).
  --min_len MIN_LEN     pat: Display only reads covering at least MIN_LEN CpG sites [1]
  --shuffle             pat: Shuffle reads order, while keeping the startCpG order (sort -k2,2n -k3,3R)
  --no_sort             pat: Keep read order, as in the original pat file
  --sub_sample SUB_SAMPLE
                        pat: subsample from reads. Only supported for pat
  -o OUT_PATH, --out_path OUT_PATH
                        Output path. [stdout]
  -np, --nanopore       BETA VERSION: pull very long reads starting before the requested region

random access (-r, -s flags)

View only reads (or values, in case of *.beta files) overlapping the specified genomic region. If no genomic region was provided, view outputs the whole file. The genomic region may be specified in one of two ways:

1. CHROM:START-END, e.g. -r chr1:10,747-10,758
2. SITE1-SITE2, e.g. -s 45-50. This is non-inclusive, i.e. only sites 45,46,47,48,49 will be considered.
   This feature uses tabix and the *.csi index to achieve efficient random access (without reading the whole pat file). For beta files, it utilizes the fact that they have fixed size, so random access takes O(1).

strict (pat)

When specified with a region(s), view trims reads crossing the borders of the region. For example:

% wgbs_tools view FILE.pat.gz -s 167-168
chr1	166	TTTTT	1
chr1	167	TTTC	1
% wgbs_tools view FILE.pat.gz -s 167-168 --strict
chr1	167	T	1
chr1	167	T	1

sub_sample (pat)

Subsamle from the pat file, sub_sample of the reads. the count field is taken into consideration. For example, if a read has count>1, it may be outputed with a smaller count.

% wgbs_tools view FILE.pat.gz -s 167-168
chr1	166	TTTTT	5
% wgbs_tools view FILE.pat.gz -s 167-168 --sub_sample .4
chr1	166	TTTTT	2