批量求fasta格式序列长度

linux下用awk计算fasta序列的长度
fasta序列文件data.fa

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>Gorai.004G111100.1
ATGGGTACTGCTCCAACCCAGTGCCCTTCTGGAATCACTGCAAATTTCCACGCCAAATTTGATAACAGAACTGAGTTTTC
>Gorai.004G111100.2
ATGTTTTTCATGCTCCGGTGGACAAGATACTCTGGGATGCCGGGGAACAGTTTTTCCTTTTCTTGGCAGACATATGCACATAAAATTCTT
>Gorai.004G111100.3
ATGGGTACTGCTCCAACCCAGTGCCCTTCTGGAATCACTGCAAATTTCCAC
>Gorai.004G111100.4
ATGGGAATGCATGAACTAGCAGCCAAAGTTGATGAGT

首先将fasta序列转换成一行显示,命令如下:

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awk '/^>/&&NR>1{print "";}{ printf "%s",/^>/ ? $0"%":$0 }'  data.fa >data2.fa

结果:

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>Gorai.004G111100.1%ATGGGTACTGCTCCAACCCAGTGCCCTTCTGGAATCACTGCAAATTTCCACGCCAAATTTGATAACAGAACTGAGTTTTC
>Gorai.004G111100.2%ATGTTTTTCATGCTCCGGTGGACAAGATACTCTGGGATGCCGGGGAACAGTTTTTCCTTTTCTTGGCAGACATATGCACATAAAATTCTT
>Gorai.004G111100.3%ATGGGTACTGCTCCAACCCAGTGCCCTTCTGGAATCACTGCAAATTTCCAC
>Gorai.004G111100.4%ATGGGAATGCATGAACTAGCAGCCAAAGTTGATGAGT

长度计算:

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awk -F"%" '{print $1"\t"length($2)}'  data2.fa >data3.fa

结果:

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>Gorai.004G111100.1 80
>Gorai.004G111100.2 90
>Gorai.004G111100.3 51
>Gorai.004G111100.4 37

More: Question: Multiline Fasta To Single Line Fasta

本文固定链接:http://tiramisutes.github.io/2015/11/08/fa-length.html 转载请注明出处!

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