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_DBSPLIT(1p)						User Contributed Perl Documentation					    BP_DBSPLIT(1p)

NAME

       dbsplit - script to split an input set of database(s) into smaller pieces

SYNOPSIS

	 dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat]
		     [--prefix outputprefix] [ < file1 file 2  OR file1 file2]

DESCRIPTION

       This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate
       files of X numbers of sequences.  You specify X with the "--size/-s" parameter.	The input and output sequence format is any that is
       supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc).

       You can specify the input data either as a single file with -i filename, or as a single file as an argument like

	 % dbsplit file1 file2

       or as a list of sequence data with

	 % cat file1 file2 file3 | dbsplit

       You'll want to use the "--prefix" to specify what the output prefix will be.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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

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