Usage:
search2gff [−o outputfile] [−f reportformat] [−i inputfilename] OR file1 file2 ..
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
Jason Stajich, jason-at-bioperl-dot-org
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.