2.2 Linux Practice

徐英泽 2024011267

返回引导页

0. 准备：解压缩文件gtf

root@bioinfo_docker:/home/test# cd /home/test/linux
root@bioinfo_docker:/home/test/linux# ls
1.gtf.gz  file
root@bioinfo_docker:/home/test/linux# gunzip 1.gtf.gz
root@bioinfo_docker:/home/test/linux# ls
1.gtf  file		#成功解压缩

1. 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）

root@bioinfo_docker:/home/test/linux#  awk '$1=="XI" && $3=="CDS"{print $0}' 1.gtf | sort -k5 -n | tail -10

XI      ensembl CDS     631152  632798  .       +       0       gene_id "YKR097W"; gene_version "1"; transcript_id "YKR097W"; transcript_version "1"; exon_number "1"; gene_name "PCK1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PCK1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR097W"; protein_version "1";
XI      ensembl CDS     633029  635179  .       -       0       gene_id "YKR098C"; gene_version "1"; transcript_id "YKR098C"; transcript_version "1"; exon_number "1"; gene_name "UBP11"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "UBP11"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR098C"; protein_version "1";
XI      ensembl CDS     635851  638283  .       +       0       gene_id "YKR099W"; gene_version "1"; transcript_id "YKR099W"; transcript_version "1"; exon_number "1"; gene_name "BAS1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "BAS1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR099W"; protein_version "1";
XI      ensembl CDS     638904  639968  .       -       0       gene_id "YKR100C"; gene_version "1"; transcript_id "YKR100C"; transcript_version "1"; exon_number "1"; gene_name "SKG1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "SKG1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR100C"; protein_version "1";
XI      ensembl CDS     640540  642501  .       +       0       gene_id "YKR101W"; gene_version "1"; transcript_id "YKR101W"; transcript_version "1"; exon_number "1"; gene_name "SIR1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "SIR1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR101W"; protein_version "1";
XI      ensembl CDS     646356  649862  .       +       0       gene_id "YKR102W"; gene_version "1"; transcript_id "YKR102W"; transcript_version "1"; exon_number "1"; gene_name "FLO10"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "FLO10"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR102W"; protein_version "1";
XI      ensembl CDS     653080  656733  .       +       0       gene_id "YKR103W"; gene_version "1"; transcript_id "YKR103W"; transcript_version "1"; exon_number "1"; gene_name "NFT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "NFT1"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR103W"; protein_version "1";
XI      ensembl CDS     656836  657753  .       +       0       gene_id "YKR104W"; gene_version "1"; transcript_id "YKR104W"; transcript_version "1"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YKR104W"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR104W"; protein_version "1";
XI      ensembl CDS     658719  660464  .       -       0       gene_id "YKR105C"; gene_version "1"; transcript_id "YKR105C"; transcript_version "1"; exon_number "1"; gene_name "VBA5"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "VBA5"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR105C"; protein_version "1";
XI      ensembl CDS     661442  663286  .       +       0       gene_id "YKR106W"; gene_version "1"; transcript_id "YKR106W"; transcript_version "1"; exon_number "1"; gene_name "GEX2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "GEX2"; transcript_source "ensembl"; transcript_biotype "protein_coding"; protein_id "YKR106W"; protein_version "1";

2. 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。

root@bioinfo_docker:/home/test/linux# grep -v '^#' 1.gtf | grep '^IV' | awk '{print $3}
'| sort | uniq -c | sort -n
    853 start_codon
    853 stop_codon
    886 gene
    886 transcript
    895 CDS
    933 exon

3. 寻找不在 IV 号染色体上的所有负链上的基因中最长的2条 CDS 序列，输出他们的长度

root@bioinfo_docker:/home/test/linux# grep -v '^#' 1.gtf | grep -v '^IV' | awk '$7=="-"&& $3=="CDS"{print $5-$4+1}' | sort -n | tail -2
12276
14730

4. 寻找 XV 号染色体上长度最长的5条基因，并输出基因 id 及对应的长度

root@bioinfo_docker:/home/test/linux# grep -v '^#' 1.gtf | grep '^\bXV\b' | awk '$3=="g
ene"{split($10,x,";");name = x[1];gsub("\"", "", name);print name,$5-$4+1}' | sort -n -
k 2 | tail -5
YOR142W-B 5269
YOR192C-B 5314
YOR343W-B 5314
YOR396W 5391
YOL081W 9240

(注意，一定要使用 \b 限定 XV 的范围，否则会匹配到 XVI 等序列 )

5. 统计1.gtf列数

root@bioinfo_docker:/home/test/linux# grep -v '^#' 1.gtf | awk -F'\t' '{print NF}' | sort -u
9

( -F'\t'为指定制表分隔符 )