Bionode
Bionode是一系列供生物信息开发者使用的模块化Javascript API和Shell命令。简单的说就是一堆node module和shell命令（由于node自身流数据的特性，将其改编成支持pipe的shell命令十分容易也很高效）。
典型的使用场景如下
# Parse sequences in a fasta file into one JSON object per line, collect the ones that match chr11 and in fasta$ cat genome.fasta | bionode-fasta | grep chr11 | bionode-fasta --write
这个项目是由Repositive.io支持的。Repositive是一个提供人类基因数据库搜索服务的公司，索引了上千个数据库。
Examples
看到页面给出的例子就懵逼了
# Download all bacteria gff files$ bionode-ncbi download gff bacteria
bacteria gff files看起来是某种细菌的数据，可是，细菌的数据是毛...
GFF File
gff格式是Sanger研究所定义，是一种简单的、方便的对于DNA、RNA以及蛋白质序列的特征进行描述的一种数据格式，比如序列的那里到那里是基因，已经成为序列注释的通用格式，比如基因组的基因预测，许多软件都支持输入或者输出gff格式。目前格式定义的最新版本是版本3。原始定义见
搜索了下，发现这领域大家很喜欢用GFF这种格式，还有v2,v3版。但还都是tab+spec来表示数据，隐隐地感觉到Bionode的价值所在=.=
Installation
安装Nodejs（废话），全局安装bionode，最好把bionode-ncbi也装上，它可以访问NCBI API (e-utils)。
npm install bionode -gnpm install bionode-ncbi -g
NCBI API (e-utils)
NCBI全称是The National Center for Biotechnology Information，美国的。网站一如既往的做的很"低调"，数据看起来很全。
国内有
搜索的过程中发现也有人在恨小心翼翼的爬NCBI，。其实NCBI早已给出了API文档，。
ClinVar
ClinVar aggregates information about genomic variation and its relationship to human health.
ClinVar是一个Star-based的记录基因变异与人体健康之间关系的数据库。换句话说就是你某个基因位变异了，80%可能你就是红绿色盲了。不过这里的数据是自愿提交的，所以数据很稀疏。
bionode xxx
装完了bionode了吧，那就可以把它当命令行工具执行一下例子啦
$ bionode ncbi search genome solenopsis invicta{"uid":"2938","organism_name":"Solenopsis invicta","organism_kingdom":"Eukaryota","organism_group":"","organism_subgroup":"Insects","defline":"Solenopsis invicta overview","projectid":49663,"project_accession":"PRJNA49663","status":"Draft","number_of_chromosomes":"0","number_of_plasmids":"0","number_of_organelles":"1","assembly_name":"Si_gnG","assembly_accession":"GCA_000188075.1","assemblyid":244018,"create_date":"2011/02/03 00:00","options":"","weight":"","chromosome_assemblies":"0","scaffold_assemblies":"1","sra_genomes":"0","taxid":13686} 返回值就是个JSON，JSer爽吧！等等，这话是啥意思...solenopsis invicta???
看来我们是GET了一下这货的基因信息。
{"uid":"2938","organism_name":"Solenopsis invicta","organism_kingdom":"Eukaryota","organism_group":"","organism_subgroup":"Insects","defline":"Solenopsis invicta overview","projectid":49663,"project_accession":"PRJNA49663","status":"Draft","number_of_chromosomes":"0","number_of_plasmids":"0","number_of_organelles":"1","assembly_name":"Si_gnG","assembly_accession":"GCA_000188075.1","assemblyid":244018,"create_date":"2011/02/03 00:00","options":"","weight":"","chromosome_assemblies":"0","scaffold_assemblies":"1","sra_genomes":"0","taxid":13686} 没有chromosomes是闹哪样...让我搜搜人的...bionode ncbi search genome human...
于是悲剧了...它...是...不只是全文搜索...连炭疽都出来了
{"organism_name":"Bacillus anthracis","projectid":12333,"project_accession":"PRJNA12333","status":"Complete","number_of_chromosomes":"1",...} 好吧，让我们只找可以相爱的智人homo sapiens。
{"uid":"51","organism_name":"Homo sapiens","organism_kingdom":"Eukaryota","organism_group":"","organism_subgroup":"Mammals","defline":"Human genome projects have generated an unprecedented amount of knowledge about human genetics and health.","projectid":9558,"project_accession":"PRJNA9558","status":"Complete","number_of_chromosomes":"48","number_of_plasmids":"0","number_of_organelles":"1","assembly_name":"GRCh38.p8","assembly_accession":"GCA_000001405.23","assemblyid":763971,"create_date":"2001/02/15 00:00","options":"","weight":1000,"chromosome_assemblies":"10","scaffold_assemblies":"31","sra_genomes":"0","taxid":9606} 啊啊啊，请叫我智障。为什么number_of_chromosomes是48啊，不是46吗！！！
就这样吧，让我冷静一下...