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)
Check Out this Related Man Page
BP_BULK_LOAD_GFF(1p) User Contributed Perl Documentation BP_BULK_LOAD_GFF(1p)NAME
bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.
SYNOPSIS
% bulk_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...
DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained in a list of GFF files and/or FASTA sequence files. You must use the
exact variant of GFF described in Bio::DB::GFF. Various command-line options allow you to control which database to load and whether to
allow an existing database to be overwritten.
This script differs from bp_load_gff.pl in that it is hard-coded to use MySQL and cannot perform incremental loads. See bp_load_gff.pl for
an incremental loader that works with all databases supported by Bio::DB::GFF, and bp_fast_load_gff.pl for a MySQL loader that supports
fast incremental loads.
NOTES
If the filename is given as "-" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.
FASTA format files are distinguished from GFF files by their filename extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files. Everything else is treated as a GFF file. If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in
gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
The nature of the bulk load requires that the database be on the local machine and that the indicated user have the "file" privilege to
load the tables and have enough room in /usr/tmp (or whatever is specified by the $TMPDIR environment variable), to hold the tables
transiently.
Local data may now be uploaded to a remote server via the --local option with the database host specified in the dsn, e.g.
dbi:mysql:test:db_host
The adaptor used is dbi::mysqlopt. There is currently no way to change this.
About maxfeature: the default value is 100,000,000 bases. If you have features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000. This value must be a power of 10.
Note that Windows users must use the --create option.
If the list of GFF or fasta files exceeds the kernel limit for the maximum number of command-line arguments, use the --long_list
/path/to/files option.
COMMAND-LINE OPTIONS
Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database.
--database <dsn> Database name (default dbi:mysql:test)
--adaptor Adaptor name (default mysql)
--create Reinitialize/create data tables without asking
--user Username to log in as
--fasta File or directory containing fasta files to load
--long_list Directory containing a very large number of
GFF and/or FASTA files
--password Password to use for authentication
(Does not work with Postgres, password must be
supplied interactively or be left empty for
ident authentication)
--maxbin Set the value of the maximum bin size
--local Flag to indicate that the data source is local
--maxfeature Set the value of the maximum feature size (power of 10)
--group A list of one or more tag names (comma or space separated)
to be used for grouping in the 9th column.
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
the load.
--Temporary Location of a writable scratch directory
SEE ALSO
Bio::DB::GFF, fast_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_BULK_LOAD_GFF(1p)