EnglishFrenchSpanish

Ad


OnWorks favicon

bp_seqfeature_loadp - Online in the Cloud

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

This is the command bp_seqfeature_loadp 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

PROGRAM:

NAME


bp_seqfeature_load.pl - Load GFF into a SeqFeature database

DESCRIPTION


Pass any number of GFF or fasta format files (or GFF with embedded fasta) to load the
features and sequences into a SeqFeature database. The database (and adaptor) to use is
specified on the command line. Use the --create flag to create a new SeqFeature database.

SYNOPSIS


bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]

Try 'bp_seqfeature_load.pl --help' or '--man' for more information.

OPTIONS


-d, --dsn
DBI data source (default dbi:mysql:test)

-n, --namespace
The table prefix to use (default undef) Allows several independent sequence feature
databases to be stored in a single database

-s, --seqfeature
The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)

-a, --adaptor
The storage adaptor (class) to use (default DBI::mysql)

-v, --verbose
Turn on verbose progress reporting (default true) Use --noverbose to switch this off.

-f, --fast
Activate fast loading. (default 0) Only available for some adaptors.

-T, --temporary-directory
Specify temporary directory for fast loading (default File::Spec->tmpdir())

-i, --ignore-seqregion
If true, then ignore ##sequence-region directives in the GFF3 file (default, create a
feature for each region)

-c, --create
Create the database and reinitialize it (default false) Note, this will erase previous
database contents, if any.

-u, --user
User to connect to database as

-p, --password
Password to use to connect to database

-z, --zip
Compress database tables to save space (default false)

-S, --subfeatures
Turn on indexing of subfeatures (default true) Use --nosubfeatures to switch this off.

--summary
Generate summary statistics for coverage graphs (default false) This can be run on a
previously loaded database or during the load. It will default to true if --create is
used.

-N, --nosummary
Do not generate summary statistics to save some space and load time (default if
--create is not specified, use this option to explicitly turn off summary statistics
when --create is specified)

--noalias-target
Don't create an Alias attribute whose value is the target_id in a Target attribute (if
the feature contains a Target attribute, the default is to create an Alias attribute
whose value is the target_id in the Target attribute)

Please see http://www.sequenceontology.org/gff3.shtml for information about the GFF3
format. BioPerl extends the format slightly by adding a ##index-subfeatures directive. Set
this to a true value if you wish the database to be able to retrieve a feature's
individual parts (such as the exons of a transcript) independently of the top level
feature:

##index-subfeatures 1

It is also possible to control the indexing of subfeatures on a case-by-case basis by
adding "index=1" or "index=0" to the feature's attribute list. This should only be used
for subfeatures.

Subfeature indexing is true by default. Set to false (0) to save lots of database space
and speed performance. You may use --nosubfeatures to force this.

Use bp_seqfeature_loadp online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    KompoZer
    KompoZer
    KompoZer is a wysiwyg HTML editor using
    the Mozilla Composer codebase. As
    Nvu's development has been stopped
    in 2005, KompoZer fixes many bugs and
    adds a f...
    Download KompoZer
  • 2
    Free Manga Downloader
    Free Manga Downloader
    The Free Manga Downloader (FMD) is an
    open source application written in
    Object-Pascal for managing and
    downloading manga from various websites.
    This is a mirr...
    Download Free Manga Downloader
  • 3
    UNetbootin
    UNetbootin
    UNetbootin allows you to create bootable
    Live USB drives for Ubuntu, Fedora, and
    other Linux distributions without
    burning a CD. It runs on Windows, Linux,
    and ...
    Download UNetbootin
  • 4
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM
    Dolibarr ERP - CRM is an easy to use
    ERP and CRM open source software package
    (run with a web php server or as
    standalone software) for businesses,
    foundations...
    Download Dolibarr ERP - CRM
  • 5
    SQuirreL SQL Client
    SQuirreL SQL Client
    SQuirreL SQL Client is a graphical SQL
    client written in Java that will allow
    you to view the structure of a JDBC
    compliant database, browse the data in
    tables...
    Download SQuirreL SQL Client
  • 6
    Brackets
    Brackets
    Brackets is a free, modern open-source
    text editor made especially for Web
    Development. Written in HTML, CSS, and
    JavaScript with focused visual tools and
    prepr...
    Download Brackets
  • More »

Linux commands

Ad