[Bioperl-l] How to run this "bp_search2gff.pl"
Dan Bolser
dan.bolser at gmail.com
Mon Mar 16 13:03:53 UTC 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:
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)
>
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