convert hdf5 (h5) files into tsv (tab seperated value) text (matrix) files.
hdf2tab/
hdf2tab.py - Extract c-data from HDF5 file into TXT (matrix.gz)
hdf2tab requires numpy/h5py
You can install the dependencies with:
for req in $(cat requirements.txt); do pip install $req; done
Download the project.
wget -O hdf2tab.zip https://github.com/blajoie/hdf2tab/archive/master.zip
Or clone the git project
[ssh] - git clone git@github.com:blajoie/hdf2tab.git
[https] - git clone https://github.com/blajoie/hdf2tab.git
Unzip the master:
unzip hdf2tab.zip
cd hdf2tab/
After installing dependencies, you should be free to use hdf2tab.py: e.g.
$ python scripts/hdf2tab.py
See the hdf2tab Wiki for full documentation of Hi-C HDF5 file format.
See the HDF5 spec Wiki for focumentation of the dekkerlab Hi-C HDF5 file format. (h5 dataset/attributes)
Download/Clone the hdf2tab.py HDF5 helper script (python).
numpy/scipy/h5py required. Python 2.7+
See the Usage Wiki for help running the hdf2tab.py scripy.
Hi-C data is pushed through the dekkerlab standard pipeline (to be available on GIT soon) and binned at multiple bin sizes (resolutions):
- 10mb
- 2.5mb
- 1mb
- 500kb
- 250kb
- 100kb
- 40kb
See the Wiki for full documentation, examples, operational details and other information.
- Bryan Lajoie
- Noam Kaplan
- Twitter: @my5C
hdf2tab can read/subset a hdf5 file containing Hi-C data into a my5C fomatted tsv matrix file.
$ python scripts/hdf2tab.py --help
usage: hdf2tab.py [-h] -i IN_FILE [-v] [--info] [-o OUT_FILE]
[-wm {cis,seperate,all}] [-z ZOOM_COORDS [ZOOM_COORDS ...]]
[-xz X_ZOOM_COORDS [X_ZOOM_COORDS ...]]
[-yz Y_ZOOM_COORDS [Y_ZOOM_COORDS ...]]
[-e BED_FILE [BED_FILE ...]]
[-xe X_BED_FILE [X_BED_FILE ...]]
[-ye Y_BED_FILE [Y_BED_FILE ...]]
[--element_exten ELEMENT_EXTEN]
[-c SELECTED_CHRS [SELECTED_CHRS ...]]
[-xc X_SELECTED_CHRS [X_SELECTED_CHRS ...]]
[-yc Y_SELECTED_CHRS [Y_SELECTED_CHRS ...]] [-b BLOCKSIZE]
[-p PRECISION] [--maxdim MAX_DIMENSION] [--outputchrs]
[--outputbins] [--outputfactors] [--version]
Extract c-data from HDF5 file into TXT (matrix.gz)
optional arguments:
-h, --help show this help message and exit
-i IN_FILE, --input IN_FILE
interaction matrix hdf5 file (default: None)
-v, --verbose Increase verbosity (specify multiple times for more)
(default: None)
--info interaction matrix hdf5 file (default: False)
-o OUT_FILE, --output OUT_FILE
interaction matrix output file (default: None)
-wm {cis,seperate,all}
write mode (cis=cis only maps, seperate=all cis/trans
seperate fiels, all=single matrix) (default: all)
-z ZOOM_COORDS [ZOOM_COORDS ...], --zoom ZOOM_COORDS [ZOOM_COORDS ...]
x/y axis zoom coordinate (default: [])
-xz X_ZOOM_COORDS [X_ZOOM_COORDS ...], --xzoom X_ZOOM_COORDS [X_ZOOM_COORDS ...]
x axis zoom coordinate (default: [])
-yz Y_ZOOM_COORDS [Y_ZOOM_COORDS ...], --yzoom Y_ZOOM_COORDS [Y_ZOOM_COORDS ...]
y axis zoom coordinate (default: [])
-e BED_FILE [BED_FILE ...], --elements BED_FILE [BED_FILE ...]
x/y axis elements bed file (bed3+ format) (default:
[])
-xe X_BED_FILE [X_BED_FILE ...], --xelements X_BED_FILE [X_BED_FILE ...]
x axis elements bed file (bed3+ format) (default: [])
-ye Y_BED_FILE [Y_BED_FILE ...], --yelements Y_BED_FILE [Y_BED_FILE ...]
y axis elements bed file (bed3+ format) (default: [])
--element_exten ELEMENT_EXTEN
bp extension for all elements, +/- bp to start/end of
each element (default: 0)
-c SELECTED_CHRS [SELECTED_CHRS ...], --chrs SELECTED_CHRS [SELECTED_CHRS ...]
x/y axis subset of chromosomes to extract (default:
[])
-xc X_SELECTED_CHRS [X_SELECTED_CHRS ...], --xchrs X_SELECTED_CHRS [X_SELECTED_CHRS ...]
x axis subset of chromosomes to extract (default: [])
-yc Y_SELECTED_CHRS [Y_SELECTED_CHRS ...], --ychrs Y_SELECTED_CHRS [Y_SELECTED_CHRS ...]
y axis subset of chromosomes to extract (default: [])
-b BLOCKSIZE, --blocksize BLOCKSIZE
block size of HDF5 file (default: None)
-p PRECISION output precision (# of digits) (default: 4)
--maxdim MAX_DIMENSION
maximum dimension of allxall matrix - else cis only
(default: 12000)
--outputchrs output the chromosome list file, no matrix output
(default: False)
--outputbins output the bin position file, no matrix output
(default: False)
--outputfactors output the balancing factor list file, no matrix
output (default: False)
--version show program's version number and exit
(dump info of HDF5 file)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 --info
(dump balance factors from HDF5 file)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 --outputfactors
-> NPC__mm9__genome__C-10000000-iced.factors
(dump genome wide tsv matrix
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -v
(dump all cis maps)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -wm cis -v
(dump cis maps for chr1, chr2 and chr3 from the HDF5 file)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -wm cis --chrs chr1 chr2 chr3 -v
-> NPC__mm9__genome__C-10000000-iced__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr2.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr3.matrix.gz
(dump chr1 (y-axis) vs genome (x-axis), single matrix)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -wm all -yc chr1 -v
-> NPC__mm9__genome__C-10000000-iced.matrix.gz
(dump chr1 (y-axis) vs genome (x-axis), seperate chr:chr matrices)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -wm seperate -yc chr1 -v
-> NPC__mm9__genome__C-10000000-iced__chr10__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr11__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr12__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr13__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr14__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr15__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr16__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr17__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr18__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr19__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr1__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr2__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr3__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr4__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr5__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr6__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr7__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr8__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chr9__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chrM__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chrX__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced__chrY__chr1.matrix.gz
-> NPC__mm9__genome__C-10000000-iced.matrix.gz
(chr1,chr2,chr3,chrX:20000000-80000000,chr7:10000000-20000000 chr8:30000000-40000000 on y-axis)
(chr4,chr5,chr6,chrX:20000000-80000000,chr9:50000000-60000000 chr10:70000000-80000000 on x-axis)
(output single matrix file as 'NPC-zoomA6253'.matrix.gz file)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -wm all -yc chr1 chr2 chr3 -xc chr4 chr5 chr6 -z chrX:20000000-80000000 -yz chr7:10000000-20000000 chr8:30000000-40000000 -xz chr9:50000000-60000000 chr10:70000000-80000000 -o NPC-zoomA6253
-> NPC-zoomA6253.matrix.gz
(subset HDF by bed file)
$ python scripts/hdf2tab.py -i test/C-10000000/iced/NPC__mm9__genome__C-10000000-iced.hdf5 -e test/chromosome-bands-qB.bed -v
-> NPC__mm9__genome__C-10000000-iced.matrix.gz
For bugs, questions and discussions please use the Github Issues.
Licensed under the Apache License, Version 2.0 (the 'License'); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an 'AS IS' BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.