OnWorks favicon

bp_load_gffp - Online in the Cloud

Run bp_load_gffp in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command bp_load_gffp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.


% bp_load_gff.pl -d testdb -u user -p pw
--dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
dna1.fa dna2.fa features1.gff features2.gff ...


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 uses the Bio::DB::GFF interface, and so works with all database adaptors
currently supported by that module (MySQL, Oracle, PostgreSQL soon). However, it is slow.
For faster loading, see the MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl

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 -

On the first load of a database, you will see a number of "unknown table" errors. This is

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, or another power of 10.


Command-line options can be abbreviated to single-letter options. e.g. -d instead of

--dsn <dsn> Data source (default dbi:mysql:test)
--adaptor <adaptor> Schema adaptor (default dbi::mysqlopt)
--user <user> Username for mysql authentication
--pass <password> Password for mysql authentication
--fasta <path> Fasta file or directory containing fasta files for the DNA
--create Force creation and initialization of database
--maxfeature Set the value of the maximum feature size (default 100 Mb; must be a 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.
--upgrade Upgrade existing database to current schema
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--quiet No progress reports
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
the load.

Use bp_load_gffp online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    TurkDevOps a?k kaynak yaz?l?m
    geli?tirici topluluklar? DevTurks-Team
    Taraf?ndan desteklenmektedir..
    Download turkdevops
  • 2
    Wine is an Open Source implementation
    of the Windows API on top of X and Unix.
    Wine provides both a development toolkit
    for porting Windows sources to Unix and...
    Download Wine
  • 3
    LAME (Lame Aint an MP3 Encoder)
    LAME (Lame Aint an MP3 Encoder)
    LAME is an educational tool to be used
    for learning about MP3 encoding. The
    goal of the LAME project is to improve
    the psycho acoustics, quality and speed
    of MP...
    Download LAME (Lame Aint an MP3 Encoder)
  • 4
    A set of Python extension modules that
    wrap the cross-platform GUI classes from
    wxWidgets.. Audience: Developers. User
    interface: X Window System (X11), Win32 ...
    Download wxPython
  • 5
    This is the Total War pack file manager
    project, starting from version 1.7. A
    short introduction into Warscape
    modding: ...
    Download packfilemanager
  • 6
    A network traffic tool for measuring
    TCP and UDP performance with metrics
    around both throughput and latency. The
    goals include maintaining an active
    iperf cod...
    Download IPerf2
  • 7
    fre:ac - free audio converter
    fre:ac - free audio converter
    fre:ac is a free audio converter and CD
    ripper for various formats and encoders.
    It features MP3, MP4/M4A, WMA, Ogg
    Vorbis, FLAC, AAC, and Bonk format
    support, ...
    Download fre:ac - free audio converter
  • More »

Linux commands