practice guide - linux
本章内容主要是学会用Linux的一些简单编程方法去查看GTF/GFF基因组注释文件的基本信息，并学会对文件中数据进行提取，利用提取到的数据计算特定feature（例如计算基因积累长度等）。
Homework
列出1.gtf文件中 XI 号染色体上的后 10 个 CDS （按照每个CDS终止位置的基因组坐标进行sort）
代码实现
grep CDS 1.gtf |awk '$1 == "XI"' | sort -t $'\t' -k 5 | tail==注意:$ 会将’\t’转置为TAB分隔符, -k 5是按照第五列也就是CDS终止位置进行排序==
`输出结果为`
```shell
XI ensembl CDS 82947 82998 . + 0 gene_id "YKL190W"; gene_version "1"; transcript_id "YKL190W"; transcript_version "1"; exon_number "1"; gene_name "CNB1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "CNB1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL190W"; protein_version "1";
XI ensembl CDS 83075 83547 . + 1 gene_id "YKL190W"; gene_version "1"; transcript_id "YKL190W"; transcript_version "1"; exon_number "2"; gene_name "CNB1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "CNB1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL190W"; protein_version "1";
XI ensembl CDS 84704 85900 . + 0 gene_id "YKL189W"; gene_version "1"; transcript_id "YKL189W"; transcript_version "1"; exon_number "1"; gene_name "HYM1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "HYM1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL189W"; protein_version "1";
XI ensembl CDS 86228 88786 . - 0 gene_id "YKL188C"; gene_version "1"; transcript_id "YKL188C"; transcript_version "1"; exon_number "1"; gene_name "PXA2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PXA2"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL188C"; protein_version "1";
XI ensembl CDS 89287 91536 . - 0 gene_id "YKL187C"; gene_version "1"; transcript_id "YKL187C"; transcript_version "1"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YKL187C"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL187C"; protein_version "1";
XI ensembl CDS 92747 93298 . - 0 gene_id "YKL186C"; gene_version "1"; transcript_id "YKL186C"; transcript_version "1"; exon_number "1"; gene_name "MTR2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MTR2"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL186C"; protein_version "1";
XI ensembl CDS 94499 96262 . + 0 gene_id "YKL185W"; gene_version "1"; transcript_id "YKL185W"; transcript_version "1"; exon_number "1"; gene_name "ASH1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "ASH1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL185W"; protein_version "1";
XI ensembl CDS 96757 98154 . + 0 gene_id "YKL184W"; gene_version "1"; transcript_id "YKL184W"; transcript_version "1"; exon_number "1"; gene_name "SPE1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "SPE1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL184W"; protein_version "1";
XI ensembl CDS 98398 98607 . - 0 gene_id "YKL183C-A"; gene_version "1"; transcript_id "YKL183C-A"; transcript_version "1"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YKL183C-A"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL183C-A"; protein_version "1";
XI ensembl CDS 98721 99638 . + 0 gene_id "YKL183W"; gene_version "1"; transcript_id "YKL183W"; transcript_version "1"; exon_number "1"; gene_name "LOT5"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "LOT5"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKL183W"; protein_version "1";
```统计 IV 号染色体上各类 feature （1.gtf文件的第3列，有些注释文件中还应同时考虑第2列） 的数目，并按升序排列
代码实现
grep -v '^#' 1.gtf |awk '$1 == "IV"{print $3}'| sort | uniq -c==grep -v ‘^#’ 是为了去除以#开头的无关项==
输出为
