linux 系统中shell实现将fasta文件的碱基转换为一行及还原

1、测试数据

root@PC1:/home/test# cat a.fna  ##  实现将碱基转换为1行， 其他信息不变
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
gataaaaaataaatagaaacaaaatcactgaagaaCCAGTGTGCCTGCTCAGGTCAGATGAAGCCAGAGGGCTGCCAGAG
GGCAAGCGAGCTGCGTTGCCTGGAAAAAGTTAAACACACAGAGAGCATGGTGGCTCTGATACTTTCTAGAAGGATTAAAG
TCACTTTCCCAGTCTTTATGAGAATTGGGCCGAAGCTTAGCTGGTGCAACGAATTTAGAAATGAATGCACTTGCATTTGA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
AGATGATGTGTCTTTGCCTTGAgctaaaaattttagaataatctgaACGTCATCTGAGGAACCTGCTTCTGGCGTGGTTT
TGGTGTCAGCATCTTCTCACCCTCTCTAGTAATTTTCAGTATGCATTTCTATTTTCGTGTAGTTATTTACAGGAGCATTT
TATGGAAAACCGGCTCAAATCTTTTTGGGTGCAGGGGTAGTTCAAATGCACTGAGACCCTCAGTTTCACTTGCTAATCTC
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTCCAGAAACCCTGTTCTCCTCGAGTGACAAGGTCAGCAGGGCAGCACGTGTGTTCCTGTCACTGCCAACTCAAGAATAT
GAAGTTTAAAGAGTTTCACCATCAAATGCAGTGTCGTGGACTGCCCCTGAACAGGTGTTTATAATCACGTGTGCAAGTGA
AGCAAGCACAAATCCTCAGTGGAAAACGGGCAGAGGACACGAGCagacaattctttttaaaaactgcacaaATTAGCACA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTAGGCACGGATGAGCGTGCCTACCGTGTTGCATGGAGGTAACAGATGCCAGAGCCCGGAGGAGGCGCAAAGCTCACAAA
CAGATGCGGACCGCAGGAAGCCGGGACGGCCTTCCTCCCCTGAAGCAGGAGGACGCGCCCTACAGAAAGCCGCTCGATCC
TCCAGGCATTTGTTGTGAGCACTTAATCATCATTCGATCATTTGACGTGTACTCACTAGTAAAAGGCAGGACTGTGTCCC

 

2、 awk + sed实现

root@PC1:/home/test# awk '{if($0 ~ /^[a-zA-Z]/) {printf("%s", $0)} else {print $0}}' a.fna | sed '$ s/$/\n/' | sed '2,$ s/>/\n>/'  
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
gataaaaaataaatagaaacaaaatcactgaagaaCCAGTGTGCCTGCTCAGGTCAGATGAAGCCAGAGGGCTGCCAGAGGGCAAGCGAGCTGCGTTGCCTGGAAAAAGTTAAACACACAGAGAGCATGGTGGCTCTGATACTTTCTAGAAGGATTAAAGTCACTTTCCCAGTCTTTATGAGAATTGGGCCGAAGCTTAGCTGGTGCAACGAATTTAGAAATGAATGCACTTGCATTTGA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
AGATGATGTGTCTTTGCCTTGAgctaaaaattttagaataatctgaACGTCATCTGAGGAACCTGCTTCTGGCGTGGTTTTGGTGTCAGCATCTTCTCACCCTCTCTAGTAATTTTCAGTATGCATTTCTATTTTCGTGTAGTTATTTACAGGAGCATTTTATGGAAAACCGGCTCAAATCTTTTTGGGTGCAGGGGTAGTTCAAATGCACTGAGACCCTCAGTTTCACTTGCTAATCTC
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTCCAGAAACCCTGTTCTCCTCGAGTGACAAGGTCAGCAGGGCAGCACGTGTGTTCCTGTCACTGCCAACTCAAGAATATGAAGTTTAAAGAGTTTCACCATCAAATGCAGTGTCGTGGACTGCCCCTGAACAGGTGTTTATAATCACGTGTGCAAGTGAAGCAAGCACAAATCCTCAGTGGAAAACGGGCAGAGGACACGAGCagacaattctttttaaaaactgcacaaATTAGCACA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTAGGCACGGATGAGCGTGCCTACCGTGTTGCATGGAGGTAACAGATGCCAGAGCCCGGAGGAGGCGCAAAGCTCACAAACAGATGCGGACCGCAGGAAGCCGGGACGGCCTTCCTCCCCTGAAGCAGGAGGACGCGCCCTACAGAAAGCCGCTCGATCCTCCAGGCATTTGTTGTGAGCACTTAATCATCATTCGATCATTTGACGTGTACTCACTAGTAAAAGGCAGGACTGTGTCCC

 

3、利用正则表达式及sed预存储还原

root@PC1:/home/test# ls
a.fna  b.fna
root@PC1:/home/test# cp b.fna b.fna_bak   ## 要在源文件进行修改，先进行备份
root@PC1:/home/test# ls
a.fna  b.fna  b.fna_bak
root@PC1:/home/test# cat b.fna
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
gataaaaaataaatagaaacaaaatcactgaagaaCCAGTGTGCCTGCTCAGGTCAGATGAAGCCAGAGGGCTGCCAGAGGGCAAGCGAGCTGCGTTGCCTGGAAAAAGTTAAACACACAGAGAGCATGGTGGCTCTGATACTTTCTAGAAGGATTAAAGTCACTTTCCCAGTCTTTATGAGAATTGGGCCGAAGCTTAGCTGGTGCAACGAATTTAGAAATGAATGCACTTGCATTTGA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
AGATGATGTGTCTTTGCCTTGAgctaaaaattttagaataatctgaACGTCATCTGAGGAACCTGCTTCTGGCGTGGTTTTGGTGTCAGCATCTTCTCACCCTCTCTAGTAATTTTCAGTATGCATTTCTATTTTCGTGTAGTTATTTACAGGAGCATTTTATGGAAAACCGGCTCAAATCTTTTTGGGTGCAGGGGTAGTTCAAATGCACTGAGACCCTCAGTTTCACTTGCTAATCTC
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTCCAGAAACCCTGTTCTCCTCGAGTGACAAGGTCAGCAGGGCAGCACGTGTGTTCCTGTCACTGCCAACTCAAGAATATGAAGTTTAAAGAGTTTCACCATCAAATGCAGTGTCGTGGACTGCCCCTGAACAGGTGTTTATAATCACGTGTGCAAGTGAAGCAAGCACAAATCCTCAGTGGAAAACGGGCAGAGGACACGAGCagacaattctttttaaaaactgcacaaATTAGCACA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTAGGCACGGATGAGCGTGCCTACCGTGTTGCATGGAGGTAACAGATGCCAGAGCCCGGAGGAGGCGCAAAGCTCACAAACAGATGCGGACCGCAGGAAGCCGGGACGGCCTTCCTCCCCTGAAGCAGGAGGACGCGCCCTACAGAAAGCCGCTCGATCCTCCAGGCATTTGTTGTGAGCACTTAATCATCATTCGATCATTTGACGTGTACTCACTAGTAAAAGGCAGGACTGTGTCCC
root@PC1:/home/test# for i in `seq 10`; do sed 's/\(^[a-zA-Z]\{50\}\)[^\n]/\1\n/' b.fna -i; done   ## 50可修改为任意的碱基数
root@PC1:/home/test# cat b.fna
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
gataaaaaataaatagaaacaaaatcactgaagaaCCAGTGTGCCTGCTC
GGTCAGATGAAGCCAGAGGGCTGCCAGAGGGCAAGCGAGCTGCGTTGCCT
GAAAAAGTTAAACACACAGAGAGCATGGTGGCTCTGATACTTTCTAGAAG
ATTAAAGTCACTTTCCCAGTCTTTATGAGAATTGGGCCGAAGCTTAGCTG
TGCAACGAATTTAGAAATGAATGCACTTGCATTTGA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
AGATGATGTGTCTTTGCCTTGAgctaaaaattttagaataatctgaACGT
ATCTGAGGAACCTGCTTCTGGCGTGGTTTTGGTGTCAGCATCTTCTCACC
TCTCTAGTAATTTTCAGTATGCATTTCTATTTTCGTGTAGTTATTTACAG
AGCATTTTATGGAAAACCGGCTCAAATCTTTTTGGGTGCAGGGGTAGTTC
AATGCACTGAGACCCTCAGTTTCACTTGCTAATCTC
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTCCAGAAACCCTGTTCTCCTCGAGTGACAAGGTCAGCAGGGCAGCACGT
TGTTCCTGTCACTGCCAACTCAAGAATATGAAGTTTAAAGAGTTTCACCA
CAAATGCAGTGTCGTGGACTGCCCCTGAACAGGTGTTTATAATCACGTGT
CAAGTGAAGCAAGCACAAATCCTCAGTGGAAAACGGGCAGAGGACACGAG
agacaattctttttaaaaactgcacaaATTAGCACA
>NC_019458.2 Ovis aries breed Texel chromosome 1, Oar_v4.0, [whole genome shotgun sequence]
CTAGGCACGGATGAGCGTGCCTACCGTGTTGCATGGAGGTAACAGATGCC
GAGCCCGGAGGAGGCGCAAAGCTCACAAACAGATGCGGACCGCAGGAAGC
GGGACGGCCTTCCTCCCCTGAAGCAGGAGGACGCGCCCTACAGAAAGCCG
TCGATCCTCCAGGCATTTGTTGTGAGCACTTAATCATCATTCGATCATTT
ACGTGTACTCACTAGTAAAAGGCAGGACTGTGTCCC