bp_search2tribe(1p) [debian man page]

BP_SEARCH2TRIBE(1p)					User Contributed Perl Documentation				       BP_SEARCH2TRIBE(1p)

NAME

       search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

SYNOPSIS

       Usage:
	 search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

DESCRIPTION

       This script is probably too slow for most people's uses.  It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output
       from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL
       with the mcxdeblast script and the --m9 option.

       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.

       The options are:

	  -o filename	       - the output filename [default STDOUT]
	  -f format	       - search result format (blast, fasta)
				 (ssearch is fasta format). default is blast.
	  -w or --weight VALUE - Change the default weight for E(0.0) hits
				 to VALUE (default=200 (i.e. 1e-200) )
	  -h		       - this help menu

       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: search2tribe < file1 file2 file3

AUTHOR

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

perl v5.14.2							    2012-03-02						       BP_SEARCH2TRIBE(1p)

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)