1.cut
cut用于文件分割，将整个文件分割成不同的字段，可以对字段进行单独的操作，类似于excel中进行列操作。
-b, 按字节（bytes）定位;-c, 按字符（characters）定位;-f, 按域（fields）定位; -d ,设置间隔符，默认制表符（Tab）。
常用-d,-f。根据文件差异，有的分隔符是空格，有的是逗号、tab键等，-f指定要选择哪列或哪些列。

cat查看文件内容，此文件以逗号分割
Cat a.txt  
SRR776504,RNA-Seq,646,8308777,PRJNA192864,SAMN01978938,24124470
SRR776504,RNA-Seq,646,8308777,PRJNA192864,SAMN01978938,24124470
SRR776505,RNA-Seq,579,26432223,PRJNA192864,SAMN01978939,78862401
SRR776505,RNA-Seq,652,26432336,PRJNA192864,SAMN01978939,78862611
SRR776505,RNA-Seq,652,26432254,PRJNA192864,SAMN01978939,78862001
SRR776506,RNA-Seq,577,24314163,PRJNA192864,SAMN01978940,72169712
cut –d ‘,’ –f 1 a.txt  
逗号分割成7部分，取第一个字段
SRR776504
SRR776504
SRR776505
SRR776505
SRR776505
SRR776506
sed 's/,/\t/g' a.txt | cut -f 1-4 
 sed命令把,替换成Tab键，再取1至4字段；
SRR776504       RNA-Seq 646     8308777
SRR776504       RNA-Seq 646     8308777
SRR776505       RNA-Seq 579     26432223
SRR776505       RNA-Seq 652     26432336
SRR776505       RNA-Seq 652     26432254
SRR776506       RNA-Seq 577     24314163
 |为管道符，用于连续操作，表示把前一条命令的结果传输给后一条命令，即前面的输出作为后面的输入

2.sort
sort用于排序，默认按字符编码排序。-k指定按哪个字段排序；使用-n参数按数字大小排序；-u用于去重复，等同于sort | uniq；；-r，反向排序（默认升序）；-t，指定分隔符
对前文取出的4个字段进行操作

先按第一列排序，再按第三列数字大小降序
sed 's/,/\t/g' a.txt | cut -f 1-4 | sort -k1,1 -k3,3nr 
SRR776504       RNA-Seq 646     8308777
SRR776504       RNA-Seq 646     8308777
SRR776505       RNA-Seq 652     26432254
SRR776505       RNA-Seq 652     26432336
SRR776505       RNA-Seq 579     26432223
SRR776506       RNA-Seq 577     24314163
其中前2行重复
sed 's/,/\t/g' a.txt | cut -f 1-4 | sort -k1,1 -k3,3nr | uniq -c
      2 SRR776504       RNA-Seq 646     8308777
      1 SRR776505       RNA-Seq 652     26432254
      1 SRR776505       RNA-Seq 652     26432336
      1 SRR776505       RNA-Seq 579     26432223
      1 SRR776506       RNA-Seq 577     24314163
#uniq用于去重，-c表示进行重复计数，计数结果显示在第一列；-d(duplication)，获得重复的行。

再比如

cat <<END | uniq -c
> a
> a
> a
> b
> c
> d
> d
> END
       cat <<END | uniq -c
      3 a
      1 b
      1 c
      2 d
cat <<END后可键盘输入内容，前面会显示>，最后输入END结束，然后统计重复情况
cat <<END | uniq -d
> a
> a
> a
> b
> c
> d
> d
> END
a
d
#最后输出重复的内容a,d

3.grep
grep用于查找，-c，计数（count）

head t.gtf #查看文件的开头部分内容，-n指定查看前多少行；-v,反向查找
#!genome-version TAIR10
#!genome-date 2008-04
#!genome-build-accession GCA_000001735.1
#!genebuild-last-updated 2010-09
1       araport11       gene    10942648        10944727        .       -       .       gene_id "AT1G30814"; gene_source "araport11"; gene_biotype "protein_coding";
1       araport11       transcript      10942648        10944727        .       -       .       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding";
1       araport11       exon    10944317        10944727        .       -       .       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; exon_number "1"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding"; exon_id "AT1G30814.1.exon1";
1       araport11       exon    10944078        10944229        .       -       .       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; exon_number "2"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding"; exon_id "AT1G30814.1.exon2";
1       araport11       CDS     10944078        10944225        .       -       0       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; exon_number "2"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding"; protein_id "AT1G30814.1";
grep "CDS" t.gtf
1       araport11       CDS     10944078        10944225        .       -       0       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; exon_number "2"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding"; protein_id "AT1G30814.1";
1       araport11       CDS     10943868        10943984        .       -       2       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; exon_number "3"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding"; protein_id "AT1G30814.1";
#"CDS"字样会标识出颜色
grep -c "CDS" t.gtf
2
grep -v "#" t.gtf | head -3 #不看注释行
1       araport11       gene    10942648        10944727        .       -       .       gene_id "AT1G30814"; gene_source "araport11"; gene_biotype "protein_coding";
1       araport11       transcript      10942648        10944727        .       -       .       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding";
1       araport11       exon    10944317        10944727        .       -       .       gene_id "AT1G30814"; transcript_id "AT1G30814.1"; exon_number "1"; gene_source "araport11"; gene_biotype "protein_coding"; transcript_source "araport11"; transcript_biotype "protein_coding"; exon_id "AT1G30814.1.exon1";
cat b.txt
snpeff
snppppef
exper
database
data2
123
*123
grep "s" b.txt
snpeff
snppppef
database
grep "^s" b.txt #匹配s开头的字符
snpeff
snppppef
grep "f$" b.txt #匹配f结尾的字符
snpeff
snppppef
grep "snp*ef" b.txt #匹配p 0次或多次
snpeff
snppppef
grep -E "^s|d" b.txt #-E,匹配正则表达，|，或表达
snpeff
snppppef
database
data2