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  • how to extract passed record from a fasta.file

    Hi,
    I have downloaded a fa.gz file, in which the records are about protein's secretion prediction. The format is like this:
    >AT1G51370 Symbols: X Chr location SecreTary:0.8 pass
    NHJAHJGHAJGKGJGHGAKJEHHGALKGJJGHGH...
    >AT1G51380 Symbols: X Chr location SecreTray:0 fail
    GKHKGMJGHGJGRJG.......

    The SecreTary value and status indicate the protein is a secretory one or not. How can I extract the all gene ID which SecreTary status is pass?

    I download the fa.gz file of Arabidopsis from https://solgenomics.net/secretom/detail/prediction

    Thanks!

  • #2
    Code:
    grep "pass$" file.fasta > headers_that_end_in_pass.txt
    Code:
    grep "pass$" file.fasta | cut -c 2- > headers_that_end_in_pass_without_the_>.txt
    Last edited by rhinoceros; 03-03-2016, 01:32 AM.
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