cooler1
Sparse, compressed, binary persistent storage
Usage
cooler [OPTIONS]
COMMAND
[ARGS] ...
Overview
Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files.
Options
-
-v, --verbose -
Verbose logging.
-
-d, --debug -
On error, drop into the post-mortem debugger shell.
-
-V, --version -
Show the version and exit.
-
-h, --help -
Show this message and exit.
Commands:
- cload
-
Create a cooler from genomic pairs and bins.
- load
-
Create a cooler from a pre-binned matrix.
- merge
-
Merge multiple coolers with identical axes.
- coarsen
-
Coarsen a cooler to a lower resolution.
- zoomify
-
Generate a multi-resolution cooler file by coarsening.
- balance
-
Out-of-core matrix balancing.
- info
-
Display a cooler's info and metadata.
- dump
-
Dump a cooler's data to a text stream.
- show
-
Display and browse a cooler in matplotlib.
- makebins
-
Generate fixed-width genomic bins.
- digest
-
Generate fragment-delimited genomic bins.
- csort
-
Sort and index a contact list.
- ls
-
List all coolers inside a file.
- cp
-
Copy a cooler from one file to another or within the same file.
- ln
-
Create a hard link to a cooler (rather than a true copy) in the...
- mv
-
Rename a cooler within the same file.
- tree
-
Display a file's data hierarchy.
- attrs
-
Display a file's attribute hierarchy.