remove the fasta sequence which doesn't contain ATGC

Question

[harry]

I have a fasta sequence in which some sequence doesn't contain "ATGC" like below so I want to remove all fasta sequences from my file which doesn't contain the proper sequence:-

>hsa-NHS_0029
partial

Thanks in advance

[cpad0112]

partial has two 'a's and one 't' in it. Try

$ seqkit -w 0 grep -srip '[ATGC]' test.fa

[harry]

it doesn't remove those fasta sequences with a header in my output file.

[cpad0112]

Please post example fasta file, code you have run and output from example fasta file.

[harry]

Below is the example fasta file in which you can see a fast sequence is "partial" which is not actually a fast sequence and I want to remove all this sequence from my fasta file with a header.

>hsa-NHS_0029
partial

>hsa-MAP3K2_0035
CAAAGCAGACACAGTCTTTTTCCTTATGGGGCTTATAGTGTGGTATTGGTGGTCTTCAAGCTTTAGGTGCATGCTCTCTAGGGGCAGCACAGGCCAGTCTTTGGGAAGTAGAAAGAAAACACTAGAATTTTAATCTTGTAAAAATATTTATTTTGGAAGTATGCCTACATGATATATGTACCCAAAAATGTTGAGTTGATAAGGATACAGAAATCAAAATTTGAATCCCTGGAGAACAACTTTATTCTTTTTAACAGTTTCATTTCATTCTGTCATACAGATGTCACATAGTTAAGTTTAATCAGTTTCCTGAATAAACATTTTGCATTGCTCTTTAACATTCATATGGTAGTTTCAGTGCAAATTAAAAACTGCAGAAAATTTTGAGAATTTCCTTTTTAAAATTTGTATTAGGATAAAACAGACTTCAGAGTTTTTGAACTTTGTGTTGAAAATGTGTGCCTGTGTTAAAAAATGTGCTGTTGTAGTGTTAAGTAAAGTGAATATTTACGTAATTTTTAGTTAATCTTGTATCACTCTAAAAGGAG

>hsa-TMOD2_0026
ATGTTGTCAAAGGTGAAAAAGTAAAGCCAGTATTTGAGGAACCACCAAATCCCACAAATGTGGAAATAAGCCTGCAGCAGATGAAAGCCAATGATCCTAGCTTGCAAGAAGTCAACCTCAACAACATTAAGTTCGTAAGAAGAGAGTTGAAGCAGACCGAAG

As you suggested a seqkit command, I ran it but it don't remove those sequences from my file.

seqkit -w 0 grep -srip '[ATGC]' test.fa >test_new.fa

So I want the output is like below :- In which the "partial" fasta sequence is removed with a header.

>hsa-MAP3K2_0035
    CAAAGCAGACACAGTCTTTTTCCTTATGGGGCTTATAGTGTGGTATTGGTGGTCTTCAAGCTTTAGGTGCATGCTCTCTAGGGGCAGCACAGGCCAGTCTTTGGGAAGTAGAAAGAAAACACTAGAATTTTAATCTTGTAAAAATATTTATTTTGGAAGTATGCCTACATGATATATGTACCCAAAAATGTTGAGTTGATAAGGATACAGAAATCAAAATTTGAATCCCTGGAGAACAACTTTATTCTTTTTAACAGTTTCATTTCATTCTGTCATACAGATGTCACATAGTTAAGTTTAATCAGTTTCCTGAATAAACATTTTGCATTGCTCTTTAACATTCATATGGTAGTTTCAGTGCAAATTAAAAACTGCAGAAAATTTTGAGAATTTCCTTTTTAAAATTTGTATTAGGATAAAACAGACTTCAGAGTTTTTGAACTTTGTGTTGAAAATGTGTGCCTGTGTTAAAAAATGTGCTGTTGTAGTGTTAAGTAAAGTGAATATTTACGTAATTTTTAGTTAATCTTGTATCACTCTAAAAGGAG

    >hsa-TMOD2_0026
    ATGTTGTCAAAGGTGAAAAAGTAAAGCCAGTATTTGAGGAACCACCAAATCCCACAAATGTGGAAATAAGCCTGCAGCAGATGAAAGCCAATGATCCTAGCTTGCAAGAAGTCAACCTCAACAACATTAAGTTCGTAAGAAGAGAGTTGAAGCAGACCGAAG

[cpad0112]

do you really have string 'partial' as your sequence? didn't understand that. Here is the solution:

$ seqkit -w 0 grep -svp "partial" test.fa

>hsa-MAP3K2_0035
CAAAGCAGACACAGTCTTTTTCCTTATGGGGCTTATAGTGTGGTATTGGTGGTCTTCAAGCTTTAGGTGCATGCTCTCTAGGGGCAGCACAGGCCAGTCTTTGGGAAGTAGAAAGAAAACACTAGAATTTTAATCTTGTAAAAATATTTATTTTGGAAGTATGCCTACATGATATATGTACCCAAAAATGTTGAGTTGATAAGGATACAGAAATCAAAATTTGAATCCCTGGAGAACAACTTTATTCTTTTTAACAGTTTCATTTCATTCTGTCATACAGATGTCACATAGTTAAGTTTAATCAGTTTCCTGAATAAACATTTTGCATTGCTCTTTAACATTCATATGGTAGTTTCAGTGCAAATTAAAAACTGCAGAAAATTTTGAGAATTTCCTTTTTAAAATTTGTATTAGGATAAAACAGACTTCAGAGTTTTTGAACTTTGTGTTGAAAATGTGTGCCTGTGTTAAAAAATGTGCTGTTGTAGTGTTAAGTAAAGTGAATATTTACGTAATTTTTAGTTAATCTTGTATCACTCTAAAAGGAG
>hsa-TMOD2_0026
ATGTTGTCAAAGGTGAAAAAGTAAAGCCAGTATTTGAGGAACCACCAAATCCCACAAATGTGGAAATAAGCCTGCAGCAGATGAAAGCCAATGATCCTAGCTTGCAAGAAGTCAACCTCAACAACATTAAGTTCGTAAGAAGAGAGTTGAAGCAGACCGAAG