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Divide each fasta sequence into fragments of 200 nucleotides

I have a multi fasta seq

>gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA
CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAACGATCGAGTG
AATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGTGACCCTGATTTGTTGTTGGG
CCGCCTCGGGAGCGTCCATGGCGGGTTTGAACCTCTAGCCCGGCGCAGTTTGGGCGCCAAGCCATATGAA
AGCATCACCGGCGAATGGCATTGTCTTCCCCAAAACCCGGAGCGGCGGCGTGCTGTCGCGTGCCCAATGA

>>gi|2765657|emb|Z78532.1|CCZ78532 C.californicum 5.8S rRNA gene and ITS1 and ITS2 DNA
CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAACAGAATATATGATCGAGTG
AATCTGGAGGACCTGTGGTAACTCAGCTCGTCGTGGCACTGCTTTTGTCGTGACCCTGCTTTGTTGTTGG
GCCTCCTCAAGAGCTTTCATGGCAGGTTTGAACTTTAGTACGGTGCAGTTTGCGCCAAGTCATATAAAGC
ATCACTGATGAATGACATTATTGTCAGAAAAAATCAGAGGGGCAGTATGCTACTGAGCATGCCAGTGAA

Divide each fasta sequence into fragments of 200 nucleotides

gene fasta
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updated by WouterDeCoster WouterDeCoster • written by pratik.me.online • pratik.me.online

Not clear what kind of fragments do you want?

For example, for fragment length = 3,

$ echo -e ">seq\nacgtnACGTN"                           
>seq
acgtnACGTN

Do you want this:

$ echo -e ">seq\nacgtnACGTN" | seqkit sliding -W 3 -s 3 -g
>seq_sliding:1-3
acg
>seq_sliding:4-6
tnA
>seq_sliding:7-9
CGT
>seq_sliding:10-12
N

Or this

$ echo -e ">seq\nacgtnACGTN" | seqkit sliding -W 3 -s 1   
>seq_sliding:1-3
acg
>seq_sliding:2-4
cgt
>seq_sliding:3-5
gtn
>seq_sliding:4-6
tnA
>seq_sliding:5-7
nAC
>seq_sliding:6-8
ACG
>seq_sliding:7-9
CGT
>seq_sliding:8-10
GTN
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written by shenwei356 shenwei356

2 answers

The seqkit package provides an answer:

seqkit sliding -s 200 -W 200 input.fasta > output.fasta
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written by James Ashmore James Ashmore

Actually, option -s/--step is needed.

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written by shenwei356 shenwei356

Ah yes thanks for correcting me

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written by James Ashmore James Ashmore

awk

 awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' inpu.fa |\
 awk -F '\t' '{x=200;S=1;L=length($2);while(S<=L) { printf(">%s (%d-%d)\n%s\n",$1,S,S+x,substr($2,S,x)); S+=(x+1);}}'
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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