bp_search2gff.1p

Langue: en

Autres versions - même langue

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 1 (Commandes utilisateur)

NAME

search2gff - Turn SearchIO parseable reports(s) into a GFF report

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.