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.IX Title "BP_SEARCH2GFF 1p"
.TH BP_SEARCH2GFF 1p "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_search2gff \- turn a SearchIO report into GFF
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Usage:
.PP
.Vb 1
\&  bp_search2gff [\-o outputfile] [\-f reportformat] [\-i inputfilename]  OR file1 file2 ..
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script will turn a SearchIO report (\s-1BLAST, FASTP, SSEARCH,
AXT, WABA\s0) into \s-1GFF.\s0
.PP
The options are:
.PP
.Vb 10
\&   \-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 \*(Aqmatch\*(Aq 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
.Ve
.PP
Additionally specify the filenames you want to process on the
command-line.  If no files are specified then \s-1STDIN\s0 input is assumed.
You specify this by doing: bp_search2gff < file1 file2 file3
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason Stajich, jason-at-bioperl-dot-org
.SH "Contributors"
.IX Header "Contributors"
Hilmar Lapp, hlapp-at-gmx-dot-net
.SS "clone_loc"
.IX Subsection "clone_loc"
Title   : clone_loc
Usage   : my \f(CW$l\fR = clone_loc($feature\->location);
Function: Helper function to simplify the task of cloning locations
           for \-\-locfunc closures.
.PP
.Vb 6
\&          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
.Ve
.SS "create_loc"
.IX Subsection "create_loc"
Title   : create_loc
Usage   : my \f(CW$l\fR = create_loc(\*(L"10..12\*(R");
Function: Helper function to simplify the task of creating locations
          for \-\-locfunc closures. Creates a location from a feature\-
          table formatted string.
.PP
Example :
Returns : A Bio::LocationI object representing the location given
          as formatted string.
Args    : A GenBank feature-table formatted string.