BP_SEARCH2GFF

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.