【sed】笔记

Day2 生信宝典sed

一.给序列起名字

ct@ehbio:~/SXBD$ cat seq
ACDGTFGGCATGCDTGD
ACDGAGCDTAGCDGTA
CAGDTAGDCTADTG
ct@ehbio:~/SXBD$ sed = seq
1
ACDGTFGGCATGCDTGD
2
ACDGAGCDTAGCDGTA
3
CAGDTAGDCTADTG
# 同时缓冲两行，但只对第一行行首操作
ct@ehbio:~/SXBD$ sed = seq | sed 'N;s/^/>/;'
>1
ACDGTFGGCATGCDTGD
>2
ACDGAGCDTAGCDGTA
>3
CAGDTAGDCTADTG

二.记忆匹配

()启动记忆匹配；\1为第一个匹配项，\2为第二个匹配项；匹配项的计数根据左括号出现的位置来定，第一个(包括起来的为\1。

ct@ehbio:~/SXBD$ echo "hah ehbio hah" | sed 's/ \(.*\) /\t\1\t\1\t/'
hah    ehbio    ehbio    hah
奇偶数行处理

ct@ehbio:~/SXBD$ echo -e "odd\neven\nodd\neven"
odd
even
odd
even

# 奇偶数行合并
ct@ehbio:~/SXBD$ echo -e "odd\neven\nodd\neven" | sed 'N;s/\n/\t/'
odd    even
odd    even

# 取出偶数行，比较简单
# 注意 n (小写)撇掉了奇数行
ct@ehbio:~/SXBD$ echo -e "odd\neven\nodd\neven" | sed -n 'n;p'
even
even

# 取出奇数行
# 先都读进去，然后替换偶数行为空值，再输出
ct@ehbio:~/SXBD$ echo -e "odd\neven\nodd\neven" | sed -n 'N;s/\n.*//;p'
odd
odd

Day1 fastq转成fasta

### cat test1.fq
@SRR400264.2496 HWI-ST216_0180:3:1101:11339:2337 length=36
CTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCC
+SRR400264.2496 HWI-ST216_0180:3:1101:11339:2337 length=36
HHHHHHHHHHHHHHHHHHGHHHHGHHGHHGHHFEHH
@SRR400264.2497 HWI-ST216_0180:3:1101:11298:2341 length=35
AGCTTTTTTTTTTCTTTTTCTTTTTTGAGATGGCA
+SRR400264.2497 HWI-ST216_0180:3:1101:11298:2341 length=35
HHHHHHHHHHHHHGHHHHHHHHHHHHDFHAF=GGF
@SRR400264.2498 HWI-ST216_0180:3:1101:11256:2344 length=33
CTGTCTTCTTCCCCAGTTCATCTGCATCTCGTT
+SRR400264.2498 HWI-ST216_0180:3:1101:11256:2344 length=33
HHHHHHHHHHHHHHHHHGGHGHHGHGHHFHHHH
@SRR400264.2499 HWI-ST216_0180:3:1101:11384:2357 length=30
ATCGATAACTAAACTTCCTTTCCATATGAC
+SRR400264.2499 HWI-ST216_0180:3:1101:11384:2357 length=30
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
@SRR400264.2500 HWI-ST216_0180:3:1101:11352:2366 length=35
CCGTAACTCTTATAAGCTAGCTTATATAAGAGCTT
+SRR400264.2500 HWI-ST216_0180:3:1101:11352:2366 length=35
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHG

### $ cat test1.fq |sed -n '1~4s/^@/>/p ;2~4p' |sed 's/ .*//'
# -n :sed 处理的行输出

>SRR400264.2496
CTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCC
>SRR400264.2497
AGCTTTTTTTTTTCTTTTTCTTTTTTGAGATGGCA
>SRR400264.2498
CTGTCTTCTTCCCCAGTTCATCTGCATCTCGTT
>SRR400264.2499
ATCGATAACTAAACTTCCTTTCCATATGAC
>SRR400264.2500
CCGTAACTCTTATAAGCTAGCTTATATAAGAGCTT