bp_genbank2gff(1p) [debian man page]
BP_GENBANK2GFF(1p) User Contributed Perl Documentation BP_GENBANK2GFF(1p) NAME
bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files. SYNOPSIS
% bp_genbank2gff.pl -d genbank -f localfile.gb % bp_genbank2gff.pl -d genbank --accession AP003256 % bp_genbank2gff.pl --accession AP003256 --stdout DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained in a either a local genbank file or an accession that is fetched from genbank. Various command-line options allow you to control which database to load and whether to allow an existing database to be overwritten. The database must already have been created and the current user must have appropriate INSERT and UPDATE privileges. The --create option will initialize a new database with the appropriate schema, deleting any tables that were already there. COMMAND-LINE OPTIONS Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database. --create Force creation and initialization of database --dsn <dsn> Data source (default dbi:mysql:test) --user <user> Username for mysql authentication --pass <password> Password for mysql authentication --proxy <proxy> Proxy server to use for remote access --stdout direct output to STDOUT --adaptor <adaptor> adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle) --viral the genome you are loading is viral (changes tag choices) --source <source> source field for features ['genbank'] EITHER --file Arguments that follow are Genbank/EMBL file names OR --gb_folder What follows is a folder full of gb files to process OR --accession Arguments that follow are genbank accession numbers (not gi!) OR --acc_file Accession numbers (not gi!) in a file (one per line, no punc.) OR --acc_pipe Accession numbers (not gi!) from a STDIN pipe (one per line) SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl AUTHOR
Scott Cain, cain@cshl.org Copyright (c) 2003 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. perl v5.14.2 2012-03-02 BP_GENBANK2GFF(1p)
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BP_PROCESS_GADFLY(1p) User Contributed Perl Documentation BP_PROCESS_GADFLY(1p) NAME
process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser SYNOPSIS
% process_gadfly.pl ./RELEASE2 > gadfly.gff DESCRIPTION
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the "correct" version of the GFF format. To use this script, download the whole genome FASTA file and save it to disk. (The downloaded file will be called something like "na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give the filename.) Do the same for the whole genome GFF annotation file (the saved file will be called something like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If you wish you can download the ZIP compressed versions of these files. Next run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file: % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database using the following command: % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff (Where "fly" is the name of the database. Change it as appropriate. The database must already exist and be writable by you!) The resulting database will have the following feature types (represented as "method:source"): Component:arm A chromosome arm Component:scaffold A chromosome scaffold (accession #) Component:gap A gap in the assembly clone:clonelocator A BAC clone gene:gadfly A gene accession number transcript:gadfly A transcript accession number translation:gadfly A translation codon:gadfly Significance unknown exon:gadfly An exon symbol:gadfly A classical gene symbol similarity:blastn A BLASTN hit similarity:blastx A BLASTX hit similarity:sim4 EST->genome using SIM4 similarity:groupest EST->genome using GROUPEST similarity:repeatmasker A repeat IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not work with earlier releases. SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl AUTHOR
Lincoln Stein, lstein@cshl.org Copyright (c) 2002 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. perl v5.14.2 2012-03-02 BP_PROCESS_GADFLY(1p)