perl script for removing sequences with "X" in them

[tusharbiot]

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

[twaddlac]

Assuming there are no 'X' in your read names:

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

[maasha]

Using Biopieces:

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

[tomc]

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

tr -d X reads.fa > filtered_reads.fa

[tusharbiot]

Thanks all! The script worked.

[krobison]

Assuming there are no 'X' in your read names:

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

Even better, remove the reliance on a dangerous assumption

perl -pe 's/X//g unless (/^>/)' reads.fa > new.reads.fa

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