How to rearrange the contig numbers and rename it in an assebly.fasta file?

Question

[Ap1438]

>1 length=424197 depth=1.05x           
ATGCATGCAGTAGCAGATGCAGAGAGACAGATAG             
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA              
ACGATGATGACCCAGTAGATGACAGTAGACAGATG            
>3 length=322465 depth=0.97x               
GTACATGGTAGCAGATGCAGAGAGACAGATAGAA      
AATAGACAGTAGACTATAGACAGTAGAGATAGAGA             
ATATAHATAHATAHAGATTHATHATACAGTATAGAT         
>4 length=313463 depth=0.87x             
CGTAGATCGTAGCAGATGCAGAGAGACAGATAGA          
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA          
ATAGCAGTAGCAGTAGCAGATGACAGATGGAGAG         
>6 length=285776 depth=0.79x               
ATGCATGCAGTAGCAGATGCAGAGAGACAGATAG           
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA         
TGATGACGATGACGATGGGTAGAACACCAGATGG        
>7 length=281883 depth=0.90x                     
ATGCATGCAGTAGCAGATGCAGAGAGACAGATAG             
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA              
GTACAGTAGACAGTAGACAGAGGGGGAGATAGGA        

I have a fasta contig file which is numbered serially but for some reasons i have to remove some contigs , which resulted in gaps in the contig serial no. as shown above i.e. it became from 1,2,3,4,5,etc to 1,3,4,6,7 and so on.

So,now i want to rearrange the contigs i.e.

1 - 1             
3 - 2            
4 - 3            
6 - 4              
7 - 5 and so on till 580 (My total contigs)    

AND rename them as

1 - Contig_0001           
2 - Contig_0002           
3 - Contig_0003 and so on till Contig_0580            

I am trying it with awk print f function with increment. But i have not succeeded till now .

Thanks for your valuable time .Can anyone help me in solving this issue.

Answer 1

[shenwei356]

Try seqkit replace:

seqkit replace -p '.+' -r 'Contig_{nr}' --nr-width 4  contigs.fasta -o renamed.fasta

Example:

$ echo -ne ">1\nactg\n>3\nACTG\n"
>1
actg
>3
ACTG

$ echo -ne ">1\nactg\n>3\nACTG\n" \
    | seqkit replace -p '.+' -r 'Contig_{nr}' --nr-width 4
>Contig_0001
actg
>Contig_0002
ACTG

[Ap1438]

Thankyou for your valuable time and suggestion. This command is working fine.

[Ap1438]

Can you please explain the command?
What if i have a file where i want to replace something in the middle of the header and the file is in proper order

>S_griseus__Contig_0001__peg_1__799__35__negative        
atgcatgc        
>S_griseus__Contig_0001__peg_2__1655__3444__posetive    
gtcgtacg    

And want to change the peg_1 to peg_0001 in this header? What command will help me solve it?

[shenwei356]

seqkit replace -p '^(.+__peg_)\d+(__.+)$' -r '${1}{nr}${2}' --nr-width 4

You need to learn more about regular expressions.

Answer 2

[cpad0112]

Try this:

$ awk '/>/ {count++; printf("%s%d%s%04d\n",">",count,"-contig_",count)} !/>/{print}' test.fa

>1-contig_0001
ATGCATGCAGTAGCAGATGCAGAGAGACAGATAG             
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA              
ACGATGATGACCCAGTAGATGACAGTAGACAGATG            
>2-contig_0002
GTACATGGTAGCAGATGCAGAGAGACAGATAGAA      
AATAGACAGTAGACTATAGACAGTAGAGATAGAGA             
ATATAHATAHATAHAGATTHATHATACAGTATAGAT         
>3-contig_0003
CGTAGATCGTAGCAGATGCAGAGAGACAGATAGA          
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA          
ATAGCAGTAGCAGTAGCAGATGACAGATGGAGAG         
>4-contig_0004
ATGCATGCAGTAGCAGATGCAGAGAGACAGATAG           
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA         
TGATGACGATGACGATGGGTAGAACACCAGATGG        
>5-contig_0005
ATGCATGCAGTAGCAGATGCAGAGAGACAGATAG             
AATAGACAGTAGACGATAGACAGTAGAGATAGAGA              
GTACAGTAGACAGTAGACAGAGGGGGAGATAGGA

[Ap1438]

This command works fine. Thank you for your valuable time and suggestion.