1BP_PROCESS_GADFLY(1) User Contributed Perl Documentation BP_PROCESS_GADFLY(1)
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6 process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version
7 suitable for the Generic Genome Browser
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10 % process_gadfly.pl ./RELEASE2 > gadfly.gff
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13 This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
14 http://www.fruitfly.org/sequence/release3download.shtml into the "cor‐
15 rect" version of the GFF format.
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17 To use this script, download the whole genome FASTA file and save it to
18 disk. (The downloaded file will be called something like
19 "na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML
20 page doesn't give the filename.) Do the same for the whole genome GFF
21 annotation file (the saved file will be called something like
22 "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If you
23 wish you can download the ZIP compressed versions of these files.
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25 Next run this script on the two files, indicating the name of the down‐
26 loaded FASTA file first, followed by the gff file:
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28 % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
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30 The gadfly.gff file and the fasta file can now be loaded into a
31 Bio::DB::GFF database using the following command:
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33 % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
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35 (Where "fly" is the name of the database. Change it as appropriate.
36 The database must already exist and be writable by you!)
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38 The resulting database will have the following feature types (repre‐
39 sented as "method:source"):
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41 Component:arm A chromosome arm
42 Component:scaffold A chromosome scaffold (accession #)
43 Component:gap A gap in the assembly
44 clone:clonelocator A BAC clone
45 gene:gadfly A gene accession number
46 transcript:gadfly A transcript accession number
47 translation:gadfly A translation
48 codon:gadfly Significance unknown
49 exon:gadfly An exon
50 symbol:gadfly A classical gene symbol
51 similarity:blastn A BLASTN hit
52 similarity:blastx A BLASTX hit
53 similarity:sim4 EST->genome using SIM4
54 similarity:groupest EST->genome using GROUPEST
55 similarity:repeatmasker A repeat
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57 IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
58 files and will not work with earlier releases.
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61 Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
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64 Lincoln Stein, lstein@cshl.org
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66 Copyright (c) 2002 Cold Spring Harbor Laboratory
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68 This library is free software; you can redistribute it and/or modify it
69 under the same terms as Perl itself. See DISCLAIMER.txt for dis‐
70 claimers of warranty.
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74perl v5.8.8 2007-05-07 BP_PROCESS_GADFLY(1)