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  • perl script for removing sequences with "X" in them

    Hi all!

    I have a multi-fasta file which was masked to remove vector contamination. This has yielded some sequences to have "X" in them (probably the one which were partially masked). I wish to remove all such sequences. Can someone help me out with a perl script for the same. I guess a perl script which was originally written to remove the sequences with " N" (a much common issue) in them, would work perfectly fine.

    Thanks a ton in advance

  • #2
    Assuming there are no 'X' in your read names:

    Code:
    perl -pe 's/X//g' reads.fa > new.reads.fa

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    • #3
      Using Biopieces:

      read_fasta -i in.fna | grab -ip X -k SEQ | write_fasta -o out.fna -x

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      • #4
        again assuming there are no 'X' in your read names (that you care about):

        tr -d X reads.fa > filtered_reads.fa
        Last edited by tomc; 04-08-2012, 10:06 AM.

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        • #5
          Thanks all! The script worked.

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          • #6
            Originally posted by twaddlac View Post
            Assuming there are no 'X' in your read names:

            Code:
            perl -pe 's/X//g' reads.fa > new.reads.fa
            Even better, remove the reliance on a dangerous assumption


            Code:
            perl -pe 's/X//g unless (/^>/)' reads.fa > new.reads.fa
            [/QUOTE]

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