RE [Gmod-gbrowse] [Fwd: [Bioperl-l] search2gff]
Scott Cain
cain at cshl.edu
Tue Jan 24 16:33:18 UTC 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.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems? Stop! Download the new AJAX search engine that makes
> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd_______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
More information about the Bioperl-l
mailing list