4 stable releases
new 1.4.0 | Apr 7, 2025 |
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1.3.0 | Apr 4, 2025 |
1.2.0 | Apr 3, 2025 |
1.1.0 | Jan 13, 2025 |
#585 in Command line utilities
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36KB
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fragtk: fragment file toolkit
fragtk
is a fast and efficient toolkit implemented in Rust for working with fragment files.
To install fragtk
, please see the installation section below.
Usage
Create region x cell matrix
A region x cell matrix can be created from a fragment file and a peak file:
fragtk matrix -f <fragments.tsv.gz> -b <peaks.bed> -c <cells.txt> -o <output>
Count fragments per cell barcode
Select cell barcodes from the fragment file according to their total count:
fragtk count -f <fragments.tsv.gz> -o <barcode_counts.tsv> -t <threshold> > barcodes.txt
Filter fragments
Filter fragments according to the cell barcodes:
fragtk filter -f <fragments.tsv.gz> -c <barcodes.txt> | bgzip -c > filtered.tsv.gz
Installation
Using cargo
cargo install fragtk
From GitHub
git clone git@github.com:stuart-lab/fragtk.git
cd fragtk; cargo install --path .
Pre-compiled binaries are also available in the release.
Man Pages
The tool includes man pages (documentation) that can be generated and installed after installation:
# generate manpages
fragtk generate-manpages --outdir /tmp/fragtk-man
# install man pages (requires sudo)
# note that this path may be different on different systems
sudo cp /tmp/fragtk-man/*.1 /usr/local/share/man/man1/
# on linux, update the manual page cache by running mandb
sudo mandb
Once installed, you can view the documentation with:
man fragtk # main command documentation
man fragtk-matrix # matrix subcommand documentation
man fragtk-count # count subcommand documentation
man fragtk-filter # filter subcommand documentation
Alternatively, you can view the man pages directly without installation:
man /tmp/fragtk-man/fragtk.1
Dependencies
~12MB
~192K SLoC