1BP_CONTIG_DRAW(1)     User Contributed Perl Documentation    BP_CONTIG_DRAW(1)
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NAME

6       search_overview -- Render a SearchIO parser report into a simple over‐
7       view graphic
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SYNOPSIS

10       search_overview -i filename [-f format] [-o outputfilename] [--labels]
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DESCRIPTION

13       This script will take any Bio::SearchIO parseable report and turn it
14       into a simple overview graphic of the report.  For our purposes we are
15       assuming BLAST and the BLAST scores when assigning colors.  Output is a
16       PNG format file.
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18       This is not intended to be an overly customized script, rather it
19       should probably just be either a quick and dirty look at a report or a
20       starting point for more complicated implementations.
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22       The color is determined by the hit score which is currently pegged to
23       the NCBI scheme which looks like this
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25        RED     E<gt>= 200
26        PURPLE  80-200
27        GREEN   50-80
28        BLUE    40-50
29        BLACK   E<lt>40
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31       Options:
32        -i/--input        The input filename, otherwise input is assumed from
33       STDIN
34        -o/--output       The output filename, this is optional, if you do not
35                          provide the output filename the script will create a
36       file
37                          using the name of the query sequence and will
38       process
39                          all the sequences in the file.  If an output file‐
40       name
41                          IS provided the script will only display an image
42       for the
43                          first one.
44        -f/--format       The SearchIO format parser to use, if not provided
45                          SearchIO will guess based on the file extension.
46        -l/--labels       Display the hit sequence name as a label in the
47       overview.
48                          For lots of sequences this will make the image very
49       long
50                          so by default it is turned off.
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AUTHOR Jason Stajich

53       Jason Stajich, jason[-at-]open-bio[-dot-]org.
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57perl v5.8.8                       2007-05-07                 BP_CONTIG_DRAW(1)