NAME

bp_search2gff - turn a SearchIO report into GFF

SYNOPSIS

Usage:

bp_search2gff [-o outputfile] [-f reportformat] [-i inputfilename]  OR file1 file2 ..

DESCRIPTION

This script will turn a SearchIO report (BLAST, FASTP, SSEARCH, AXT, WABA) into GFF.

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: bp_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 Bio::LocationI object representing the location given as formatted string. Args : A GenBank feature-table formatted string.