update-sequence-db [options] <sequence database directory>
Download sequence databases.
Creates a SQLite database called
downloads sequences from multiple sources while storing information
about the sequences in the database.
The program will start in status display mode where it will give regular updates on what it is doing. You can switch it to command mode by pressing Enter. In command mode you can type the two basic commands "help" which will show the available commands and "status" which will switch it back to status mode. While sequences are downloading you may use the command "exit" to stop any further downloading.
The folder to store downloaded database files. The MEME Suite expects
to find sequence databases in a folder called
either inside in the folder
MEME Install Folder/db or in
the folder specified to the configure script
--with-db DB Install Folder . Depending on how
you configured the MEME Suite you should either specify
MEME Install Folder/db/fasta_databases or
DB Install Folder/fasta_databases .
By default, all of the standard sequence databases supported by the
MEME Suite will be updated. Specifying one or more specific types
of databases overrides this default, and then only the specified types
of sequence database will be updated. You can also specify individual
types of database to omit using the
X is one of the allowed database types (see
the section "Select Databases to Update", below).
The program creates a folder called
downloads and a folder
logs. It also creates a SQLite database called
fasta_db.sqlite. Every sequence database that is downloaded
is initially put in the folder
downloads until it has been
completely downloaded. When the sequence has been downloaded it will be
decompressed or merged from multiple sources as required and put into
a sequence file with either a
extension for protein or DNA sequences. Once the sequence has been
expanded it will be processed by
calculate a 1st order background model in a file with the extension
calculate the number of sequences, the shortest, longest and average size
and all this information will be stored in the SQLite database.
Configuration files that tweak the behaviours of the sequence database
downloaders will be automatically generated in the
subdirectory within the specified sequence database directory.
Additionally the miscellaneous source downloader will check the
conf/ subdirectory for any files ending with the extension
.csv which it reads to determine sequence sources. The MEME
Suite includes two files
db_other_genomes.csv in the distribution's
folder which may be moved into the
conf folder, though
this is not done automatically during install.
|--help||Display a help message and exit.||Run like normal.|
|Select Databases to Update|
|--[no_]ensembl||[Do not] update genomes from Ensembl.||Update all sequence databases.|
|--[no_]genbank||[Do not] update genomes from GenBank.||Update all sequence databases.|
|--[no_]ucsc||[Do not] update the genomes from UCSC.||Update all sequence databases.|
|--[no_]rsat||[Do not] update the upstream sequence databases from RSAT.||Update all sequence databases.|
|--[no_]epd||[Do not] update the Eukaryotic Promoter Database.||Update all sequence databases.|
|--[no_]misc||[Do not] update the miscellaneous sequence databases specified
||Update all sequence databases.|
|--updater||classname||Experimental Specify the classname of a custom updater.|
|--obsolete||file pattern||Mark any sequence databases that match the given glob syntax file pattern as obsolete causing them to be hidden from the interface. This option may be repeated to specify multiple patterns. After the files are obsoleted the updater exits.||Run as normal.|
|--delete_old||Sequence databases marked as obsolete (on a previous update) will be deleted.||Sequence databases marked as obsolete will be left untouched.|
|--retain_missing||Database entries for missing files are retained.||Database entries for missing files are removed.|
|--csv:directory||Create a csv file and index file that lists all the databases to enable backwards compatibility with older releases. The directory to create the csv and index file can be specified if desired but if it is not specified then the csv and index file will be placed in the sequence database directory.||Don't create a csv or index file.|
|--bin||directory||Specify the location to find the fasta-get-markov tool.||The program will search the configured bin directory and if fasta-get-markov is not present it will search the path.|
|--log||log file||Specify the file to write logs.||A log will be written the
|-v||log level||Specify the logging level [1-8].||A default logging level of 3 is used which outputs errors, warnings and summary information.|
|--priors||tsv file||Specify a tab separated values file listing all the priors that should be listed in the database. The updater will exit after changing the priors. Note that pre-existing priors will be removed!||Run as normal.|
MCAST and FIMO support priors for sequence databases but adding them is still a manual process. The process will probably be automated in future however until then this is how you add priors.
priors.distwhich you should rename in a way that makes sense.
gzipon each of the files. This should leave them with the extension ".gz" - it is important that you leave this extension so they can be ungzip-ed by the webservice script later.
|Sequence File||The path to the sequence file relative to the sequence database directory.|
|Wig File||The path to the gzip-ed ".wig" file relative to the sequence database directory.|
|Dist File||The path to the gzip-ed ".dist" file relative to the sequence database directory.|
|Biosample||A short descriptive name for the sample used in the experiment that the priors were derived from.|
|Assay||A short descriptive name for the experiment that the priors were derived from.|
|Source||A short descriptive name of the lab or group that performed the experiment that the priors were derived from.|
|URL||A URL linking to further information on the experiment.|
|Description||A description of the experiment which may contain HTML.|
As well as downloading the sequence files from many sources, the updater tracks the files using a SQLite database. The schema of the database is given below.
|id||INTEGER||PRIMARY KEY||A auto-generated unique identifier for the category. Other tables reference this field.|
|name||TEXT||UNIQUE NOT NULL||The unique name of the category as shown to users.|
|id||INTEGER||PRIMARY KEY||A auto-generated unique identifier for the listing. Other tables reference this field.|
|categoryId||INTEGER||NOT NULL REFERENCES tblCategory (id)||The identifier of the category that contains this listing.|
|name||TEXT||NOT NULL||The name of the listing shown to users.|
|description||TEXT||NOT NULL||The description of the listing shown to users.|
The combination of the fields
name is unique.
|id||INTEGER||PRIMARY KEY||A auto-generated unique identifier for the sequence file.|
|retriever||INTEGER||NOT NULL||An identifier for the code module that downloaded this sequence. It allows the individual code modules to ensure they don't change the records of files downloaded by other modules.|
|listingId||INTEGER||NOT NULL REFERENCES tblListing (id)||The identifier of the listing that contains this sequence file.|
|alphabet||INTEGER||NOT NULL CHECK (alphabet IN (1, 2, 4))||Represents the alphabet as powers of 2 so they can be combined into a bitset.
|edition||INTEGER||NOT NULL||A machine readable version. This field is used for sorting. Larger numbers are considered newer.|
|version||TEXT||NOT NULL||A human readable version which is displayed to the user.|
|description||TEXT||NOT NULL||The description of the sequence file, often containing information about the source.|
|fileSeq||TEXT||UNIQUE NOT NULL||The relative path to the sequence file.|
|fileBg||TEXT||UNIQUE NOT NULL||The relative path to the background file.|
|sequenceCount||INTEGER||NOT NULL||The number of sequences.|
|totalLen||INTEGER||NOT NULL||The total end-to-end combined length of the sequences.|
|minLen||INTEGER||NOT NULL||The length of the shortest sequence.|
|maxLen||INTEGER||NOT NULL||The length of the longest sequence.|
|avgLen||REAL||NOT NULL||The average length of the sequences.|
|stdDLen||REAL||NOT NULL||Currently unused! Intended to store the standard deviation of the average length.|
|obsolete||INTEGER||DEFAULT 0||Used to flag sequences as obsolete. Sequences flagged as obsolete are hidden from the interface.|
The combination of the fields
edition is unique.
|id||INTEGER||PRIMARY KEY||A auto-generated unique identifier for the prior.|
|sequenceId||INTEGER||NOT NULL REFERENCES tblSequenceFile (id)||The identifier of the sequence that is associated with this prior.|
|filePrior||TEXT||UNIQUE NOT NULL||The relative path to the wig file (which may be gzipped).|
|fileDist||TEXT||UNIQUE NOT NULL||The relative path to the dist file (which may be gzipped).|
|biosample||TEXT||NOT NULL||A short descriptive name for the sample used in the experiment that the priors were derived from.|
|assay||TEXT||NOT NULL||A short descriptive name for the experiment that the priors were derived from.|
|source||TEXT||NOT NULL||A short descriptive name of the lab or group that performed the experiment that the priors were derived from.|
|url||TEXT||NOT NULL||A URL linking to further information on the experiment.|
|description||TEXT||NOT NULL||A description of the experiment which may contain HTML.|