bp_mask_by_search(1p) [debian man page]

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

NAME

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

SYNOPSIS

	 mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa

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 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'

       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 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 v5.14.2							    2012-03-02						     BP_MASK_BY_SEARCH(1p)

BP_SEARCH2GFF(1p)					User Contributed Perl Documentation					 BP_SEARCH2GFF(1p)

NAME

       search2gff - Turn SearchIO parseable reports(s) into a GFF report

SYNOPSIS

       Usage:
	 search2gff [-o outputfile] [-f reportformat] [-i inputfilename]  OR file1 file2 ..

DESCRIPTION

       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH, AXT, WABA) into a GFF File.

       The options are:

	  -i infilename      - (optional) inputfilename, will read
			       either ARGV files or from STDIN
	  -o filename	     - the output filename [default STDOUT]
	  -f format	     - search result format (blast, fasta,waba,axt)
			       (ssearch is fasta format). default is blast.
	  -t/--type seqtype  - if you want to see query or hit information
			       in the GFF report
	  -s/--source	     - specify the source (will be algorithm name
			       otherwise like BLASTN)
	  --method	     - the method tag (primary_tag) of the features
			       (default is similarity)
	  --scorefunc	     - a string or a file that when parsed evaluates
			       to a closure which will be passed a feature
			       object and that returns the score to be printed
	  --locfunc	     - a string or a file that when parsed evaluates
			       to a closure which will be passed two
			       features, query and hit, and returns the
			       location (Bio::LocationI compliant) for the
			       GFF3 feature created for each HSP; the closure
			       may use the clone_loc() and create_loc()
			       functions for convenience, see their PODs
	  --onehsp	     - only print the first HSP feature for each hit
	  -p/--parent	     - the parent to which HSP features should refer
			       if not the name of the hit or query (depending
			       on --type)
	  --target/--notarget - whether to always add the Target tag or not
	  -h		     - this help menu
	  --version	     - GFF version to use (put a 3 here to use gff 3)
	  --component	     - generate GFF component fields (chromosome)
	  -m/--match	     - generate a 'match' line which is a container
			       of all the similarity HSPs
	  --addid	     - add ID tag in the absence of --match
	  -c/--cutoff	     - specify an evalue cutoff

       Additionally specify the filenames you want to process on the command-line.  If no files are specified then STDIN input is assumed.  You
       specify this by doing: search2gff < file1 file2 file3

AUTHOR

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

Contributors
       Hilmar Lapp, hlapp-at-gmx-dot-net

   clone_loc
	Title	: clone_loc
	Usage	: my $l = clone_loc($feature->location);
	Function: Helper function to simplify the task of cloning locations
		  for --locfunc closures.

		  Presently simply implemented using Storable::dclone().
	Example :
	Returns : A L<Bio::LocationI> object of the same type and with the
		  same properties as the argument, but physically different.
		  All structured properties will be cloned as well.
	Args	: A L<Bio::LocationI> compliant object

   create_loc
	Title	: create_loc
	Usage	: my $l = create_loc("10..12");
	Function: Helper function to simplify the task of creating locations
		  for --locfunc closures. Creates a location from a feature-
		  table formatted string.

	Example :
	Returns : A L<Bio::LocationI> object representing the location given
		  as formatted string.
	Args	: A GenBank feature-table formatted string.

perl v5.14.2							    2012-03-02							 BP_SEARCH2GFF(1p)