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BP_SEARCH2GFF

SYNOPSIS

Usage:
search2gff [−o outputfile] [−f reportformat] [−i inputfilename] OR file1 file2 ..

DESCRIPTION

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

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 L<Bio::LocationI> object representing the location given
           as formatted string.
 Args    : A GenBank feature−table formatted string.
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