extract a DNA sequence based on header in multifasta file

Question

[Optimist]

Hello all,

My multifasta file with rRNA sequences looks like this.

>16S_rRNA::1:4-522(-)
TGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGCGTGATGGCGGGAACTCAAAGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGCGTATACAAAGGGAAGCGACCCCGCGAGGGCAAGCGGAACTCATAAAGTACGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTCCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTT
>16S_rRNA::0-508(-)
TTGACGTTACCGACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTGATTGAGTCAGATGTGAAATCCCCGGGCTTAACCCGGGAATTGCATCTGATACTGGTCAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCT
>5S_rRNA::1-80(-)
TGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTG
>5S_rRNA::1-77(-)
TGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGT
>5S_rRNA::1:4731-4814(-)
TGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGTGAGAGTAGGGAACCGCC

I want to extract only 16S_rRNA sequences into a new file. Is there a way to do this and I have to apply this on a large dataset of 500 files.

Thanking You

Answer 1

[cpad0112]

Try:

$ awk '$0 ~ /^>16S_rRNA/ {getline seq; print $0,seq}' test.fa
$ sed -n '/^>16S_rRNA/{N;p}' test.fa

don't use sed -i

[Optimist]

Thanks for the trick. awk has worked for me.