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BP_MASK_BY_SEARCH(1)  User Contributed Perl Documentation BP_MASK_BY_SEARCH(1)

       bp_mask_by_search - mask	sequence(s) based on its alignment results

SYNOPSIS -f blast genomefile blastfile.bls	> maskedgenome.fa

       Mask sequence based on significant alignments of	another	sequence.  You
       need to provide the report file and the entire sequence data which you
       want to mask.  By default this will assume you have done	a TBLASTN (or
       TFASTY) and try and mask	the hit	sequence assuming you've provided the
       sequence	file for the hit database.  If you would like to do the
       reverse and mask	the query sequence specify the -t/--type query flag.

       This is going to	read in	the whole sequence file	into memory so for
       large genomes this may fall over.  I'm using DB_File to prevent keeping
       everything in memory, one solution is to	split the genome into pieces
       (BEFORE you run the DB search though, you want to use the exact file
       you BLASTed with	as input to this program).

       Below the double	dash (--) options are of the form --format=fasta or
       --format	fasta or you can just say -f fasta

       By -f/--format I	mean either are	acceptable options.  The =s or =n or
       =c specify these	arguments expect a 'string'

	   -f/--format=s    Search report format (fasta,blast,axt,hmmer,etc)
	   -sf/--sformat=s  Sequence format (fasta,genbank,embl,swissprot)
	   --hardmask	    (booelean) Hard mask the sequence
			    with the maskchar [default is lowercase mask]
	   --maskchar=c	    Character to mask with [default is N], change
			    to 'X' for protein sequences
	   -e/--evalue=n    Evalue cutoff for HSPs and Hits, only
			    mask sequence if alignment has specified evalue
			    or better
	   --outfile=file   Output file	to save	the masked sequence to.
	   -t/--type=s	    Alignment seq type you want	to mask, the
			    'hit' or the 'query' sequence. [default is 'hit']
	   --minlen=n	    Minimum length of an HSP for it to be used
			    in masking [default	0]
	   -h/--help	    See	this help information

AUTHOR - Jason Stajich
       Jason Stajich, jason-at-bioperl-dot-org.

perl v5.32.1			  2019-12-07		  BP_MASK_BY_SEARCH(1)


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