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

Dan Bolser dan.bolser at gmail.com
Mon Mar 16 09:03:53 EDT 2009

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:

         search2gff [-o outputfile] [-f reportformat] [-i inputfilename]  OR
       file1 file2 ..

       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

       Jason Stajich, jason-at-bioperl-dot-org

       Hilmar Lapp, hlapp-at-gmx-dot-net


        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


        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)


> 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

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