geftools : Tools for manipulating GEFs

For a full documentation, see geftools GitHub page.

Installation

To install stereopy from source, you need:

• HDF5 1.12.1 or newer with development headers
• OpenCV 4.5.4 or newer with development headers
• A C compiler

You can specify build options for geftools as environment variables when you build it from source:

git clone https://github.com/STOmics/geftools.git
cd geftools
HDF5_ROOT=/path/to/hdf5 OpenCV_DIR=/path/to/opencv cmake .
make
make install

The supported build options are:

• HDF5_ROOT: To specify where to find HDF5.
• OpenCV_DIR: To specify where to find OpenCV.
• CMAKE_INSTALL_PREFIX: Install directory used by make install.
• GEFTOOLS_BUILD_DOC: Option to build documentation.

LIST OF COMMANDS

Command: bgef          Generate common bin GEF(.bgef) according to gem file or bin1 GEF
         cgef          Generate cell bin GEF(.cgef) according to common bin GEF and mask file
         view          View GEF

COMMANDS AND OPTIONS

geftools bgef [OPTION...]

  -i, --input-file FILE   input gene expression matrix file(.gem/.gem.gz) or bin1 bGEF file [request]
  -o, --output-file FILE  output bin GEF file (.bgef) [request]
  -b, --bin-size STR      Set bin size by the comma-separated list [request] (default: 1,10,20,50,100,200,500)
  -r, --region STR        Restrict to a rectangular region. The region is represented by the comma-separated list of
                          two vertex coordinates (minX,maxX,minY,maxY) (default: "")
  -t, --threads INT       number of threads (default: 8)
  -s, --stat    BOOL      create stat group (default: true)
  -O, --omics   STR       input omics[request]
  -v, --verbose           Verbose output
      --help              Print help

Create bgef example:

  ./geftools bgef -i xxx.bgef/xxx.bgem -b 1,10,20 -o xx.cgef -t 5 -O Transcriptomics

geftools cgef [OPTION...]

Generate cell bin GEF (.cgef) according to common bin GEF (.bgef) file and mask file

  -i, --input-file FILE   input bin GEF file [request]
  -m, --mask-file FILE    input mask file [request]
  -o, --output-file FILE  output cell bin GEF file (.cgef) [request]
  -b, --block FILE        Pre block size (default: 256,256)
  -t, --threads INT       number of threads
  -v, --verbose           Verbose output
      --help              Print help

Create cgef example:

  ./geftools cgef -i xxx.bgef -m xxx.tif -o xx.cgef -t 5

geftools view [OPTION...]

Show the contents of cell bin GEF

  -i, --input-file FILE     Input bGEF/cGEF file [request]
  -o, --output-gem FILE     Output gem file (default: stdout)
  -d, --exp_data FILE       Input bGEF file to get exp_data.
  -b, --bin-size INT        Set bin size for bgef file, just support bGEF.
  -s, --serial-number STR   Input Serial number [request]
  -e, --exon INT            whether or not output exon (default: 1)
  --help                Print help

Create bgem example:

  ./geftools view -i xxx.bgef -o xxx.gem -s SS200000135TL_D1 

Create cgem example:

  ./geftools view -i xxx.cgef -d xxx.bgef -o xxx.gem -s SS200000135TL_D1 

Coding Style Guide

See here.