RE [Gmod-gbrowse] [Fwd: [Bioperl-l] search2gff]

Scott Cain cain at cshl.edu
Tue Jan 24 11:33:18 EST 2006


Hello Dea,

If there were a bioperl parser for Geneseqer output, it probably
wouldn't be that hard to write one, but as far as I can tell there isn't
a parser (a quick grep through bioperl-live came up empty).

Sorry,
Scott


On Tue, 2006-01-24 at 17:19 +0100, dea.giardella at biogemma.com wrote:
> Hello,
> 
> In the same way are there any scripts to convert Geneseqer output in GGF3 
> format ?
> Geneseqer : http://www.plantgdb.org/PlantGDB-cgi/GeneSeqer/PlantGDBgs.cgi
> 
> Thanks a lot !
> 
> Déa GIARDELLA
> dea.giardella at biogemma.com 
> 
> 
> 
> Scott Cain <cain at cshl.edu> 
> Envoyé par : gmod-gbrowse-admin at lists.sourceforge.net
> 24/01/2006 16:26
> 
> A
> "Gbrowse (E-mail)" <gmod-gbrowse at lists.sourceforge.net>
> cc
> 
> Objet
> [Gmod-gbrowse] [Fwd: [Bioperl-l] search2gff]
> 
> 
> 
> 
> 
> 
> Hello all,
> 
> Hilmar Lapp posted the attached message to the bioperl mailing list
> about search2gff, a script for converting BLAST output to GFF3.  I
> thought it might be of interest to readers of this mailing list as well.
> 
> Scott
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
> 
> ----- Message de Hilmar Lapp <hlapp at gmx.net> sur Thu, 19 Jan 2006 15:11:22 
> -0800 -----
> Pour:
> bioperl-l <bioperl-l at bioperl.org>
> Objet:
> [Bioperl-l] search2gff
> I added a couple of capabilities to the scripts/utilities/search2gff
> script written by Jason. In a nutshell, there are now options for
> controlling the score, location, and method of the HSP-representing
> feature, as well as options for printing of parent, which parent, and
> whether to skip all except the first HSP for each hit.
> 
> As for possible applications, for example using these options you can
> blast SNP assay primers and use the options to create SNP features for
> a single basepair at the end of the primer, ready to be piped to a
> GBrowse GFF3 loader.
> 
> I tried to preserve the original functionality in its entirety, i.e.,
> if you don't use any of the new options the script should work as
> before. If not please let me know.
> 
> POD is attached.
> 
>    -hilmar
> --
> ----------------------------------------------------------
> : Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
> ----------------------------------------------------------
> 
> 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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> 
> 
> 
> 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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