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  • Script to make sequences equal length

    Hi!
    I would like to perform a motif analysis with my ChIP-Seq data on meme-suite.
    The program requires me to put in sequences of equal length.
    I have the nucleotide sequences from the regions where our protein of interest bound to in ChIP-Seq. These regions are of varying length.
    I would like to make them of equal length by figuring out the sequence of greatest length and adding 'N's to both ends of the remaining sequences.
    Anyone done this/has a R script?
    Many thanks for your feedback in advance!

  • #2
    This does not "add to both ends", I think I need a little more information to do that.

    Here's a solution that appends "N"s.
    It's not R, it's an awk "one liner" (a long one liner) :

    cat yourseqfile | awk '{ a[count++] = $0; if (length($0)>l)l=length($0) } END { for (i=0; i<count; i++) { printf("%s",a[i]); for (j=length(a[i]); j<l; j++) printf "N"; printf("\n"); } }'

    example:
    bash-3.2$ cat yourseqfile
    START

    A
    ACGTACGTACGTACGTACGTACGT
    ACGTACGTACGTAC
    ACGT
    DONE

    bash-3.2$ cat yourseqfile | awk '{ a[count++] = $0; if (length($0)>l)l=length($0) } END { for (i=0; i<count; i++) { printf("%s",a[i]); for (j=length(a[i]); j<l; j++) printf "N"; printf("\n"); } }'
    STARTNNNNNNNNNNNNNNNNNNN
    NNNNNNNNNNNNNNNNNNNNNNNN
    ANNNNNNNNNNNNNNNNNNNNNNN
    ACGTACGTACGTACGTACGTACGT
    ACGTACGTACGTACNNNNNNNNNN
    ACGTNNNNNNNNNNNNNNNNNNNN
    DONENNNNNNNNNNNNNNNNNNNN
    Last edited by Richard Finney; 10-05-2018, 06:18 AM.

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