#GTF/GFF格式# gffread入门使用

首先了解一下GTF/GFF的格式
https://asia.ensembl.org/info/website/upload/gff.html
两者的关系如下

GTF (gene transfer format) is identical to GFF (general feature format) version 2

• GFF格式主要是用来注释基因组
• GTF主要是用来对基因进行注释，比如基因在染色体上的位置（coordinate）及这段区间的其他信息。
  两者在内容上前八列相同，最后一列信息显示不一致，gff文件格式如下：

1. seqid - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seq ID must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below. (id，一般为chr或者scanfold编号)
2. source - name of the program that generated this feature, or the data source (database or project name) (注释的来源，如果未知用.代替)
3. type - type of feature. Must be a term or accession from the SOFA sequence ontology (注释信息的类型，比如Gene、cDNA、mRNA、CDS等)
4. start - Start position of the feature, with sequence numbering starting at 1.
5. end - End position of the feature, with sequence numbering starting at 1.
6. score - A floating point value. (序列相似性比对时的E-values值或者基因预测是的P-values值，“.”表示为空)
7. strand - defined as + (forward) or - (reverse).(正反义链)
8. phase - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on. (CDS类型中指出该值，值为CDS的起始位置，除以3得到的余数)
9. attributes - A semicolon-separated list of tag-value pairs, providing additional information about each feature. Some of these tags are predefined, e.g. ID, Name, Alias, Parent - see the GFF documentation for more details. (以多个键值对组成的注释信息描述，键与值之间用“=”，不同的键值用“；)

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安装如下：

  cd /some/build/dir
  git clone https://github.com/gpertea/gclib
  git clone https://github.com/gpertea/gffread
  cd gffread
  make

程序是c++编写的因此并不需要预装一些包，当然也可以使用conda安装。

conda install gffread -y

使用的例子如下：

#下载gtf/gff文档及hg19文件
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gff3.gz
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
#使用gunzip及tar分别解压，并合并下载内容获得hg19.fa
cat *.fa >hg19.fa
#根据hg19.fa提取CDS序列
gffread gencode.v19.annotation.gff3 -g hg19.fa -y tr_cds.fa
#翻译后蛋白序列
gffread gencode.v19.annotation.gff3 -g hg19.fa -x cds.fa
#获得外显子序列
gffread gencode.v19.annotation.gff3 -g hg19.fa -w exons.fa
#格式转换
gffread gencode.v19.annotation.gff3 -T -o gencode.v19.gtf
gffread merged.gtf -o- > merged.gff3

程序非常简约，通过man gffread查看使用说明
github地址 https://github.com/gpertea/gffread