[Bioperl-l] Fwd: How to run this "bp_search2gff.pl"

[Jason Stajich]

redirecting message again.

Begin forwarded message:

> From: Dan Bolser <dan.bolser at gmail.com>
> Date: March 16, 2009 6:05:19 AM PDT
> To: jason at bioperl.org
> Subject: Fwd: [Bioperl-l] How to run this "bp_search2gff.pl"
>
> Ajay?
>
>
> ---------- Forwarded message ----------
> From: Dan Bolser <dan.bolser at gmail.com>
> Date: 2009/3/16
> Subject: Re: [Bioperl-l] How to run this "bp_search2gff.pl"
> To: bioperl-l at lists.open-bio.org
>
>
> 2009/3/5 ajay <jason at bioperl.org>:
>> Respected sir,
>>
>>
>> good morning! sir my self ajay a resercher in the  
>> bioinformatics ,sir please
>> guide me how to run this bioperl scripts
>>
>> sir i have compleated the local BLAST P serch  of 255 fasta files  
>> and the
>> blast result  was saved in the (.txt) format  sir  i need to  
>> convert the
>> blast result to GFF3 format using this script "bp_search2gff.pl"
>>
>>
>> but i can not understand how to  input my BLAST result file and get  
>> the
>> output file in the  GFF3 format
>>
>> so please tell me  the steps  to input the blast result file
>>
>> what changes i have to made in the program
>
> If you run "bp_search2gff.pl -h" you get the following output, which
> should help answer your question:
>
> 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  
> com-
>       mand-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.
>
> perl v5.8.8                       2009-01-14                   
> BP_SEARCH2GFF(1)
>
>
> Dan.
>
>> sir plesae help me
>> i sahll be very thankfull to you
>>
>>
>> waiting for your kind responce
>>
>> sincerly your!s
>> Ajay
>>
>>
>>
>>
>>
>> Ajay Kumar Mahato
>> (Research Associate)
>> National Research Centre for Plant Biotechnology (IARI)
>> (http://www.nrcpb.org)
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>

Jason Stajich
jason at bioperl.org