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.IX Title "SEARCH_OVERVIEW 1p"
.TH SEARCH_OVERVIEW 1p "2012-02-20" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
search_overview \-\- Render a SearchIO parser report into a simple overview graphic
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
search_overview \-i filename [\-f format] [\-o outputfilename] [\-\-labels]
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script will take any Bio::SearchIO parseable report and turn it
into a simple overview graphic of the report.  For our purposes we are
assuming \s-1BLAST\s0 and the \s-1BLAST\s0 scores when assigning colors.  Output is
a \s-1PNG\s0 format file.
.PP
This is not intended to be an overly customized script, rather it
should probably just be either a quick and dirty look at a report or a
starting point for more complicated implementations.
.PP
The color is determined by the hit score which is currently pegged to the \s-1NCBI\s0 
scheme which looks like this
.PP
.Vb 5
\& RED     E<gt>= 200 
\& PURPLE  80\-200
\& GREEN   50\-80
\& BLUE    40\-50
\& BLACK   E<lt>40
.Ve
.PP
Options:
 \-i/\-\-input        The input filename, otherwise input is assumed from \s-1STDIN\s0
 \-o/\-\-output       The output filename, this is optional, if you do not
                   provide the output filename the script will create a file
                   using the name of the query sequence and will process
                   all the sequences in the file.  If an output filename
                   \s-1IS\s0 provided the script will only display an image for the 
                   first one.
 \-f/\-\-format       The SearchIO format parser to use, if not provided
                   SearchIO will guess based on the file extension.
 \-l/\-\-labels       Display the hit sequence name as a label in the overview.
                   For lots of sequences this will make the image very long
                   so by default it is turned off.
.SH "AUTHOR Jason Stajich"
.IX Header "AUTHOR Jason Stajich"
Jason Stajich, jason[\-at\-]open\-bio[\-dot\-]org.