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split multiple fasta into codons

Hi,

I have a list of gene sequence 

 >2619859165 

GCGTATCCGCGGTACGGCTGGCTTGGCGCGAAGGAACGTTCCCGGGACAC
CCTGTCCGGCCTCACCCTGATGGGTGTCCGTCTCTACGACCCCAACCTCG
GTCGCTTCCTCCAGACCGATCCGGTCCCCGGCGGGTCGGACAACGCCTAC

>2619859164

ATGGAGGATCTACTCTTCTCTCTATTTGGCGTGCTGATGATTAGTGCTGG
GCTGATCTCGCTTCTGATTCCCGAGAGAGTATCTCGTTGGAATGACACGG
TAGGGCCGAGGTGGATCCGCGACTTCAGTGTGCGTGGCGAGTTCAAGGCA


>2619859163 

ATGGCCGGGTGTGAGGAACAGGTGGGGATTGGCGGGTCGGGTGACGGCGT
GCCGGTCGGGTCGGTTGTCCGGTGGGGGTTGGCGACGTTCGGCACGGGGC

and I want to split the each sequence into their codons. Like

>2619859165
GCG
TAT
CCG
...
>2619859164
ATG
GAG
GAT
...

how to do this...please suggest..

thanks in advance

sequence
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by indrani.sarkar89 • indrani.sarkar89

1 answer

linearize the fasta and use sed to insert a carriage return after the codon

cat input.fasta |\
awk '/^>/ {printf("%s%s\n",(N==0?"":"\n"),$0);N++;next;} {printf("%s",$0);}END{printf("\n");}' |\
sed -e $'/^[^>]/s/\([A-Z][A-Z][A-Z]\)/\\1\\\n/g'
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written by Pierre Lindenbaum Pierre Lindenbaum

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