Rename Fasta header by Regular expression

I want the chromosome number to be kept, and the content after the only "space" is all removed.

>Chr01:10181894..10189044_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Ale:Ty1-RT ID=Chr01:10181894..10189044_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Ale:Ty1-RT;gene=RT;clade=Ale;evalue=2.7e-66;coverage=26.1;probability=0.98

>Chr02:12852689..12856792_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Ivana:Ty1-RT ID=Chr02:12852689..12856792_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Ivana:Ty1-RT;gene=RT;clade=Ivana;evalue=2.3e-107;coverage=83.3;probability=0.99

>Chr05:11339854..11345668_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Angela:Ty1-RT ID=Chr05:11339854..11345668_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Angela:Ty1-RT;gene=RT;clade=Angela;evalue=6.1e-41;coverage=31.8;probability=0.93

>Chr01_Ale 

>Chr02_Ivana

>Chr05_Angela

regular expression

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updated 3.6 years ago by shenwei356

• written 3.6 years ago by 炎峰 •

1 answer

This is something you could have fun deciphering yourself by playing with regex. But if you're giving the fun away, this works on your example:

perl -pe 's/>(\w+):.*\/.*\/.*\/(.*):.*/>$1_$2/' input.fa > output.fa

• 0 views • link

written 3.6 years ago by seidel