1.cut
cut用于文件分割，將整個文件分割成不同的字段，可以對字段進行單獨的操作，類似于excel中進行列操作。
-b, 按字節(jié)（bytes）定位;-c, 按字符（characters）定位;-f, 按域（fields）定位; -d ,設置間隔符，默認制表符（Tab）。
常用-d,-f。根據(jù)文件差異，有的分隔符是空格，有的是逗號、tab鍵等，-f指定要選擇哪列或哪些列。

cat查看文件內(nèi)容，此文件以逗號分割
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  
逗號分割成7部分，取第一個字段
SRR776504
SRR776504
SRR776505
SRR776505
SRR776505
SRR776506
sed 's/,/\t/g' a.txt | cut -f 1-4 
 sed命令把,替換成Tab鍵，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
 |為管道符，用于連續(xù)操作，表示把前一條命令的結果傳輸給后一條命令，即前面的輸出作為后面的輸入

2.sort
sort用于排序，默認按字符編碼排序。-k指定按哪個字段排序；使用-n參數(shù)按數(shù)字大小排序；-u用于去重復，等同于sort | uniq；；-r，反向排序（默認升序）；-t，指定分隔符
對前文取出的4個字段進行操作

先按第一列排序，再按第三列數(shù)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行重復
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表示進行重復計數(shù)，計數(shù)結果顯示在第一列；-d(duplication)，獲得重復的行。

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后可鍵盤輸入內(nèi)容，前面會顯示>，最后輸入END結束，然后統(tǒng)計重復情況
cat <<END | uniq -d
> a
> a
> a
> b
> c
> d
> d
> END
a
d
#最后輸出重復的內(nèi)容a,d

3.grep
grep用于查找，-c，計數(shù)（count）

head t.gtf #查看文件的開頭部分內(nèi)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"字樣會標識出顏色
grep -c "CDS" t.gtf
2
grep -v "#" t.gtf | head -3 #不看注釋行
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開頭的字符
snpeff
snppppef
grep "f$" b.txt #匹配f結尾的字符
snpeff
snppppef
grep "snp*ef" b.txt #匹配p 0次或多次
snpeff
snppppef
grep -E "^s|d" b.txt #-E,匹配正則表達，|，或表達
snpeff
snppppef
database
data2