1SEARCH_OVERVIEW(1) User Contributed Perl Documentation SEARCH_OVERVIEW(1)
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6 search_overview -- Render a SearchIO parser report into a simple
7 overview graphic
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10 search_overview -i filename [-f format] [-o outputfilename] [--labels]
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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
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37 using the name of the query sequence and will
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39 all the sequences in the file. If an output
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41 IS provided the script will only display an image
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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
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50 so by default it is turned off.
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53 Jason Stajich, jason[-at-]open-bio[-dot-]org.
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57perl v5.12.0 2010-04-29 SEARCH_OVERVIEW(1)