>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.
2 answers
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
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?
seqkit replace -p '^(.+__peg_)\d+(__.+)$' -r '${1}{nr}${2}' --nr-width 4
You need to learn more about regular expressions.
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
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