Provided by: bioperl_1.7.2-2_all bug


       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.