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 youve 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. Im 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
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
--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