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PretextSnapshot

Commandline image generator for Pretext contact maps.

Bioconda

All commandline Pretext tools for Unix (Linux and Mac) are available on bioconda.<br/>

The full suite of Pretext tools can be installed with

> conda install pretext-suite

Or, just PretextSnapshot can be installed with

> conda install pretextsnapshot

Usage

PretextSnapshot -m map.pretext --sequences "sequences to image" [other options] <br/> PretextSnapshot --help for a full list of options. <br/> PretextSnapshot --sequenceHelp for how to format the sequence specification string. <br/>

Examples

PretextSnapshot -m map.pretext --sequences "=full" :: Generates an image of the whole contact map.<br/> PretextSnapshot -m map.pretext --sequences "=all" :: Generates an image of each sequence in the contact map.<br/> PretextSnapshot -m map.pretext --sequences "seq_0" :: Generates an image of the sequence named "seq_0".<br/> PretextSnapshot -m map.pretext --sequences "seq_0, seq_1" :: Generates an image of "seq_0" and an image of "seq_1".<br/> PretextSnapshot -m map.pretext --sequences "seq_0 > seq_10" :: Generates an image between "seq_0" and "seq_10".<br/> PretextSnapshot -m map.pretext --sequences "{seq_0, seq_1}":: Generates an image of the inter-sequence region between "seq_0" and "seq_1".<br/>

Requirments, running

4 cpu cores <br/> (30 * output image size) + 6M RAM, i.e. if your output resolution is set to 1K (1024 pixels) your memory requirments will be (30 * 1K * 1K) + 6M = 36M

Third-Party acknowledgements

PretextSnapshot uses the following third-party libraries:<br/>

• AVIR image resizing algorithm designed by Aleksey Vaneev<br/>
• avx_mathfun.h<br/>
• sse_mathfun.h<br/>
• kgetopt.h<br/>
• libdeflate<br/>
• mpc<br/>
• stb_image_write.h<br/>
• stb_sprintf.h

Installation

Requires:

• clang >= 11.0.0
• meson >= 0.57.1

git submodule update --init --recursive
env CXX=clang meson setup --buildtype=release --unity on --prefix=<installation prefix> builddir
cd builddir
meson compile
meson test
meson install