1BP_PROCESS_SGD(1) User Contributed Perl Documentation BP_PROCESS_SGD(1)
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6 process_sgd.pl - Massage SGD annotation flat files into a version
7 suitable for the Generic Genome Browser
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10 % process_sgd.pl chromosomal_features.tab > yeast.gff
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13 This script massages the SGD sequence annotation flat files located at
14 ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
15 into a version of the GFF format suitable for display by the generic
16 genome browser.
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18 To use this script, get the SGD chromosomal_features.tab file from the
19 FTP site listed above, and run the following command:
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21 % process_sgd.pl chromosomal_features.tab > yeast.gff
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23 The yeast.gff file can then be loaded into a Bio::DB::GFF database
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26 % bulk_load_gff.pl -d <databasename> yeast.gff
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29 Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
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32 Lincoln Stein, lstein@cshl.org
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34 Copyright (c) 2002 Cold Spring Harbor Laboratory
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36 This library is free software; you can redistribute it and/or modify it
37 under the same terms as Perl itself. See DISCLAIMER.txt for
38 disclaimers of warranty.
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42perl v5.12.0 2010-04-29 BP_PROCESS_SGD(1)