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bashbioinformaticsfasta

Writing a single sequence from a file in FASTA format

Given a file in FASTA format (your.file), for example:

>Code1234_length1
ABCEDLKSDJFABCEDLKSDJFABCEDLKSDJFABCEDLKSDJFABCEDLKSDJF
>Code1335_length2
AJDHIEUNAJDHIEUNAJDHIEUNAJDHIEUNAJDHIEUNAJDHIEUN

But the content after >Code1234_length1 is unknown (in this example it was known just for a reproducible sample). I would like to get the unknown contents after >Code1234_length1, including the string >Code1234_length1 but before the next > and output it in a new file. i.e.

>Code1234_length1
ABCEDLKSDJFABCEDLKSDJFABCEDLKSDJFABCEDLKSDJFABCEDLKSDJF

How could this be done? Thank you.

Solution

  • If awk is your option, would you please try:

    awk '
    /^>Code1234_length1/ {f = 1; print; next}   # if the keyword is found, set the flag,
                                                #    print the line and continue with the next line
    f {                                         # if the flag is set
        if (/^>/) f = 0                         #    if next ">" is found, reset the flag
        else print                              #    otherwise print the line
    }
' your.file > new.file

    It works even if multiple lines follow the >Code1234_length1 line.