Christopher Fields > BioPerl-1.6.921 > bp_search2gff


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  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

Contributors ^

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.

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