bp_search2gff - turn a SearchIO report into GFF
bp_search2gff [-o outputfile] [-f reportformat] [-i inputfilename] OR file1 file2 ..
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
Jason Stajich, jason-at-bioperl-dot-org
Hilmar Lapp, hlapp-at-gmx-dot-net
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
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.