Modify Fasta header
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0
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6.1 years ago
utkarsh.sood ▴ 40

Hello 

I have a fasta file with sequence headers written as 

>0|quiver|1..2075|-

>0|quiver|2210..3058|-

>0|quiver|3112..4169|-

and so on till around 1000 sequences

I want to modify these as 

>1|quiver_1|1..2075|-

>2|quiver_2|2210..3058|-

>3|quiver_3|3112..4169|-

and so on

 

Please help

sequence fasta • 1.4k views
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3
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6.1 years ago
awk -F '|' '/>/ {i++;printf(">%d|%s_%d|%s|%s\n",i,$2,i,$3,$4,$5);next;} {print;}' input.fa
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Thanks for your help!

I also have one more query, please solve it.

can I modify the following headers

>gi|392981410|ref|NC_018080|pseudocap|273_483_2027_+
>gi|392981410|ref|NC_018080|pseudocap|273_2056_3159_+

so on

to

>protein 1 [Pseudomonas aeruginosa 19BR]
>protien 2 [Pseudomonas aeruginosa 19BR]

so on

thanks!

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ask this as a new question + show us what you have already tried.

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