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.IX Title "BP_MASK_BY_SEARCH 1p"
.TH BP_MASK_BY_SEARCH 1p "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
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.SH "NAME"
bp_mask_by_search \- mask sequence(s) based on its alignment results
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  bp_mask_by_search.pl \-f blast genomefile blastfile.bls > maskedgenome.fa
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
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 \s-1TBLASTN\s0
(or \s-1TFASTY\s0) 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.
.PP
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 (\s-1BEFORE\s0 you run the \s-1DB\s0 search though, you want to use the exact
file you BLASTed with as input to this program).
.PP
Below the double dash (\-\-) options are of the form
\&\-\-format=fasta or \-\-format fasta
or you can just say
\&\-f fasta
.PP
By \-f/\-\-format I mean either are acceptable options.  The =s or =n
or =c specify these arguments expect a 'string'
.PP
Options:
    \-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
    \-o/\-\-out/
    \-\-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 \s-1HSP\s0 for it to be used 
                     in masking [default 0]
    \-h/\-\-help        See this help information
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Jason Stajich, jason-at-bioperl-dot-org.