bp_search2alnblocks(1p) [debian man page]

BP_SEARCH2ALNBLOCKS(1p) 				User Contributed Perl Documentation				   BP_SEARCH2ALNBLOCKS(1p)

NAME

       search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks

SYNOPSIS

	 search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
	 blast file2.blast ...> out.fas

DESCRIPTION

       This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments
       based on the HSPs.  Note this can only work if the input file parsed contains the necessary.

       Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes
       (E.Rivas).

OPTIONS

	--maxevalue   Maximum E-value for an HSP
	--minevalue   Minimum E-value for an HSP
	--minlen      Minimum length of an HSP [default 0]
	--maxid       Maximum Percent Id [default 100]
		      (to help remove sequences which are really close)
	--minid       Minimum Percent Identity for an HSP [default 0]
	-i/--input    An optional input filename (expects input on STDIN by default)
	-o/--output   An optional output filename (exports to STDOUT by default)
	-f/--format   Specify a different Search Alignment format-
		      {fasta, axt, waba, blast, blastxml} are all permitted
		      although the format must have actual alignment
		      sequence for this script to work
		      See L<Bio::SearchIO> for more information.
	-of/--outformat Output format for the alignment blocks, anything
		      L<Bio::AlignIO> supports.
	-v/--verbose  Turn on debugging

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

perl v5.14.2							    2012-03-02						   BP_SEARCH2ALNBLOCKS(1p)

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)