how to change the header of input file
3
1
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6.9 years ago
Raghav ▴ 100

I have a fasta file input, I want change the header in my way like

>AGP1      
AAAAAAAAAAAACTCAAAAG
>CRK25      
AAAAAAAAAAAACTTTGAACTTGCTT
>AT5G27080    
AAAAAAAAAAAAGAAAGAA
>AT1G12620    
AAAAAAAAAAACAAATT
       
 

I want out put in this way

>chromosome1

AAAAAAAAAAAACTCAAAAG

>chromosome2

AAAAAAAAAAAACTTTGAACTTGCTT

change all the header in input file with chromosome

and chromosome number like chromosome1 , chromosome2...  is equal to number of headers present in input file.

is there way to resolve this problem by using sed awk or shell script?

please suggest me

thank you in advance

 

header fasta file sed awk • 1.9k views
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2
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6.9 years ago
Whoknows ▴ 860

Hi take a look at the

Renaming Entries In A Fasta File

hope it helps,

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1
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6.9 years ago
$ awk 'BEGIN { seqIdx = 0; } { if (/^>/) { print ">chromosome"seqIdx; seqIdx++; } else { print $0; } }' in.fa > out.fa
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Dear Sir Alex thank you for your fruitful suggestions.

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6.9 years ago
JC 12k

Perl One Liner:

perl -nle '(/>/) ? print ">chromosome" . ++$n : print' < FileIn.fa > FileOut.fa

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Dear Sir JC thank you for your fruitful suggestions.

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