https://github.com/cmdcolin/maf2bed

Converts multiple alignment format (MAF) files to a bed file for tabixing
https://github.com/cmdcolin/maf2bed

Last synced: 4 days ago
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Converts multiple alignment format (MAF) files to a bed file for tabixing

• Host: GitHub
• URL: https://github.com/cmdcolin/maf2bed
• Owner: cmdcolin
• Created: 2023-11-01T06:52:28.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2023-12-30T01:21:24.000Z (11 months ago)
• Last Synced: 2024-04-15T02:14:36.615Z (7 months ago)
• Language: Rust
• Size: 13.7 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md

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README

        
# maf2bed

Used to convert multiple alignment format (MAF) files to a bed tabix-y style

format. Used in jbrowse mafviewer plugin

https://github.com/cmdcolin/jbrowse-plugin-mafviewer

## Install

```

cargo install maf2bed

maf2bed --help

```

## Usage

Make sure to specify the 'assembly name' being used as the reference for the

bed file as the first argument to maf2bed

Example

```

export LC_ALL=c # improves sorting speed

#parallel compression/decompression

pigz -dc file.maf.gz | maf2bed hg19 | sort -k1,1 -k2,2n | bgzip -@8 > file.bed.gz

tabix file.bed.gz

```

Might be able to remove the sort/LC_ALL=c in some cases, but sorting ensures

that it will be ready for tabix

## Footnote 1

Converted to rust from perl as a coding exercise mostly, gaining a modest

speedup on the way https://twitter.com/cmdcolin/status/1719608993310486883

## Footnote 2

There are likely many ways to end up with a MAF file, but one way is to export the MAF from a pangenome graph

This page discusses some examples

https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#using-the-hal-output

using "--dupeMode all" is, afaik, recommended for the purposes of the JBrowse 2 mafviewer plugin, because using "--dupeMode single" can cause missing blocks of data

## Motivation

I wanted to try using the bigMaf (bigBed based) format ecosystem with large MAF

files but bedToBigBed doesn't support streaming or reading compressed files(?),

so that requires reading big files on disk and in memory. in contrast, MAF

tabix type approach like implemented here can be compressed and streaming which

allows much lower memory usage and disk space