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

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 v5.14.1			  2011-07-22		      BP_SEARCH2GFF(1)
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