bigwig2h5ΒΆ
Description:
Import a bigWig file to HDF5 format h5 file
============================================
bigWig file can be converted into gcMapExplorer compatible HDF5 file using
this tool. This HDF5 file can be loaded into gcMapExplorer browser for
interactive visualization.
Requirements
============
1) bigWigToWig : It converts binary bigWig file to ascii Wig file.
2) bigWigInfo : It fetches the information about chromosomes from bigWig file.
Both tools can be downloaded from http://hgdownload.cse.ucsc.edu/admin/exe/
for linux and Mac platform. However, these tools are not yet available for
Windows OS.
Path to these tools can be set using gcMapExplorer configure utility or can be
given with the command.
Resolutions
===========
By default, original data are downsampled to following resolutions: '1kb',
'2kb', '4kb', '5kb', '8kb', '10kb', '20kb', '40kb', '80kb', '100kb', '160kb',
'200kb', '320kb', '500kb', '640kb', and '1mb'.
The data are downsampled at this stage only to speed up the visualization
process as downsampling might slow down the interactive visualization.
Downsampling/Coarsening method
==============================
Presently, six methods are implemented:
1) min -> Minimum value
2) max -> Maximum value
3) amean -> Arithmatic mean or average
4) hmean -> Harmonic mean
5) gmean -> Geometric mean
6) median -> Median
All these methods are used by default.
See below help for "-dm/--downsample-method" option to change the methods.
To keep original 1 base resolution data
=======================================
By default, the output h5 file does not contain original 1-base resolution
data to reduce the file size. To keep the original data in h5 file, used
-ko/--keep-original flag.
Usage:
usage: gcMapExplorer bigwig2h5 [-h] [-i input.bigWig] [-t "Genomic Dataset"]
[-b2w bigWigToWig] [-binfo bigWigInfo]
[-r "List of Resolutions"] [-icn CHROMNAME]
[-dm "List of downsampling method"]
[-cmeth lzf] [-o out.h5] [-ow] [-ko]
[-wd /home/rajendra/deskForWork/scratch]
Optional arguments:
-h, --help show this help message and exit
-i input.bigWig, --input input.bigWig
Input bigWig file.
-t "Genomic Dataset", --title "Genomic Dataset"
Title of the dataset.
-b2w bigWigToWig, --bigWigToWig bigWigToWig
Path to bigWigToWig tool.
This is not neccessary when bigWigToWig path is already set using gcMapExplorer
configure utility.
It can be downloaded from http://hgdownload.cse.ucsc.edu/admin/exe/
for linux and Mac platform.
-binfo bigWigInfo, --bigWigInfo bigWigInfo
Path to bigWigInfo tool.
This is not neccessary when bigWigInfo path is already set using gcMapExplorer
configure utility.
It can be downloaded from http://hgdownload.cse.ucsc.edu/admin/exe/
for linux and Mac platform.
-r "List of Resolutions", --resolutions "List of Resolutions"
Additional input resolutions other than these resolutions: 1kb', '2kb',
'4kb', '5kb', '8kb', '10kb', '20kb', '40kb', '80kb', '100kb', '160kb','200kb',
'320kb', '500kb', '640kb', and '1mb'.
Resolutions should be provided in comma seprated values. For Example:
-r "25kb, 50kb, 75kb"
-icn CHROMNAME, --input-chromosome CHROMNAME
Input Chromosome Name.
If this is provided, only this chromosome data is extracted and stored in h5
file.
-dm "List of downsampling method", --downsample-method "List of downsampling method"
Methods to coarse or downsample the data for converting from 1-base
to coarser resolutions. If this option is not provided, all six methods (see
above) will be considered. User may use only subset of these methods.
For example: -dm "max, amean" can be used for downsampling by only these
two methods.
-cmeth lzf, --compression-method lzf
Data compression method in h5 file.
-o out.h5, --out out.h5
Output h5 file.
If file is already present, it will replace the data. Therefore, be careful
if a file with same name is present.
-ow, --overwrite If a output file is already present, overwrite the datasets in the output
file.
-ko, --keep-original To copy original 1-base resolution data in h5 file. This will increase the
file size significantly.
-wd /home/rajendra/deskForWork/scratch, --work-dir /home/rajendra/deskForWork/scratch
Directory where temporary files will be stored.