dmtools view

Description

The DM format is a binary file format that is suitable for use with computer programs, and DMtools is a powerful operating tool that can perform a range of analysis tasks on this format. However, since the DM format is difficult for humans to read, we may need to convert it into a more user-friendly text format.

To convert the DM format to text format, we can use the "dmtools view" command. We need to specify the input file as a DM file using the "-i" option. We can then choose to output the results to a specified file or directly to the front-end, using the UNIX STDOUT convention and the redirection operator (">"). Moreover, we can also select the output information content, such as whether to include positive and negative chains.

You can view and process dm file with dmtools:

Usage

$ dmtools view -i mutant.methratio.dm | head
  #Chr1     34      35      0.600000        5       -       CHG
  #Chr1     80      81      0.333333        6       -       CHH
  #Chr1     116     117     1.000000        4       -       CG
  #Chr1     117     118     0.250000        4       -       CHG

obtained text format methylation results

Parameters

-i input DM file

-o output file [stdout]

-r region for view, can be seperated by space. chr1:1-2900 chr2:1-200

--chr chromosome for view

--bed bed file for view, format: chrom start end (strand).

--strand [0/1/2] strand for show, 0 represent '+' positive strand, 1 '-' negative strand, 2 '.' all information

--context [0/1/2/3] context for show, 0 represent 'C/ALL' context, 1 'CG' context, 2 'CHG' context, 3 'CHH' context.

--mincover >= minumum coverage show, default: 0

--maxcover <= maximum coverage show, default: 10000

--outformat txt or dm format [txt]

--zl The maximum number of zoom levels. [0-10], valid for dm out

-h|--help

Tip

For feature requests or bug reports please open an issue on github.