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Ⅰ. 插件描述

Reverse-complement sequence search plugin for Vim

Ⅱ. 基本信息

创建日期：  2016-05-22 使用用户：  1 Github星：  1 插件作者：  Steve Pettitt

Ⅲ. 安装方法

使用Vundle管理器安装

在你的.vimrc下添加:

Plugin 'stveep/biovim'

… 然后在Vim中运行以下命令:

:source %
:PluginInstall

对于Vundle版本 < 0.10.2，请用上面的Bundle替换Plugin。

使用NeoBundle管理器安装

在你的.vimrc下添加:

NeoBundle 'stveep/biovim'

… 然后在Vim中运行以下命令:

:source %
:NeoBundleInstall

使用VimPlug管理器安装

在你的.vimrc下添加:

Plug 'stveep/biovim'

… 然后在Vim中运行以下命令:

:source %
:PlugInstall

使用Pathogen管理器安装

在终端中运行以下命令:

cd ~/.vim/bundle
git clone https://github.com/stveep/biovim

Ⅳ. 文档说明

##Using vim with DNA sequences

Installation

Install using Pathogen.

cd ~/.vim/bundle
git clone https://github.com/stveep/biovim.git

Vim needs to be compiled with ruby support. vim --version | grep ruby should show +ruby. Many vim installations have this by default.

Reverse-complement sequence search

Run as follows, e.g. to search for NGG or CCN:

:Biorc NGG

Or in a vimscript, :call Rcsearch("NGG"); or from ruby BioVim.rcsearch("NGG").

This works by converting the search string to a case-insensitive regexp containing the supplied and reverse-complemented string. Results will highlight if hlsearch is set (:set hlsearch).

In-place reverse complementation

To activate this functionality, add the following lines to your ~/.vimrc file. If you don't have a similar line setting up a 'leader' character, add this:

let mapleader = ","

This sets the 'leader' character to the comma (,). Add the following lines to map the reverse complement operator command to R.

nnoremap <leader>R :set operatorfunc=RcOperator<cr>g@
vnoremap <leader>R :<c-u>call RcOperator(visualmode())<cr>

Restart vim. Now you can reverse complement sequences either using conventional movement operations in vim (hjkl, w, b etc.):

,R<movement>

If your leader character is different, replace the comma with your custom leader. e.g. ,Rw will reverse-complement up until the start of the next "word". ,R2l will reverse-complement the following two bases.

Alternatively, select sequence using visual line (shift-v) or character (v) modes and type the ,R command.

Lucky BLAT searching

Basic BLAT searching of visual (character or line) highlighted sequence is supported via UCSC's "I'm feeling Lucky" BLAT search. Currently only human hg38 without hacking.

Add to ~/.vimrc:

nnoremap <leader>L :set operatorfunc=LuckyBlat<cr>g@
vnoremap <leader>L :<c-u>call LuckyBlat(visualmode())<cr>
nnoremap <leader>B :set operatorfunc=LuckyBlatURL<cr>g@
vnoremap <leader>B :<c-u>call LuckyBlatURL(visualmode())<cr>

Select sequence as for in-place reverse complement above. ,L prints the location of the top BLAT hit as a message (use :messages to view history). ,B opens default browser with the genomic location of the top BLAT hit.

AGAGCGGGCGCGCCTCTTGCAAGAAATGCAGCGA

shift-V,L 
# =>BLAT: AGAGCGGGCGCGCCTCTTGCAAGAAATGCAGCGA^@
#Position: chr1:226407853-226407886
shift-V,B
# => opens browser with UCSC location above

This is a quick and dirty search that ignores other equally good or near matches - use at own risk!

For more details see plugin/test directory.