emit_canonical_encodings.pl File Reference
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| public | usage () |
Function Documentation
◆ usage()
| public usage | ( | ) |
Undocumented method
Code:
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sub usage {
print "
Example usage: perl emit_canonical_encodings.pl -dbhost host -dbuser user
-dbpass *** -dbname dbname -dbport 3306 -transcript ENST00019112
Example usage: perl emit_canonical_encodings.pl -dbhost host -dbuser user
-dbpass *** -dbname dbname -dbport 3306 -gene ENSG00019111
Script options:
-dbname Database name
-dbhost Database host
-dbport Database port
-dbuser Database user
-dbpass Database password
Optional DB connection arguments:
-dnadbname DNA Database name
-dnadbhost DNA Database host
-dnadbuser DNA Database user
-dnadbport DNA Database port
-dnadbpass DNA Database pass
-ccdsdbname CCDS database name
-ccdshost CCDS database host
-ccdsuser CCDS database user
-ccdspass CCDS database pass
-ccdsport CCDS database port
Search params:
-transcript The transcript stable ID to use to find the gene in question
-gene The gene stable ID to emit encoded transcripts for
A warning about not using CCDS is perfectly acceptible when not running on
Human, Mouse and Zebrafish.
";
}
Undocumented method
Code:
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sub usage {
print <<EOS
Example usage: perl set_canonical_transcripts.pl -dbhost host -dbuser user
-dbpass *** -dbname dbname -dbport 3306 -coord_system toplevel -write
Script options:
-dbname Database name
-dbhost Database host
-dbport Database port
-dbuser Database user
-dbpass Database password
Optional DB connection arguments:
-dnadbname DNA Database name
-dnadbhost DNA Database host
-dnadbuser DNA Database user
-dnadbport DNA Database port
-dnadbpass DNA Database pass
-ccdsdbname CCDS database name
-ccdshost CCDS database host
-ccdsuser CCDS database user
-ccdspass CCDS database pass
-ccdsport CCDS database port
Other optional arguments:
-coord_system_name Coordinate system to use
-include_non_ref Specify if the non_reference regions should
be _excluded_. (default: include)
-include_duplicates Specify if the duplicate regions should be
_included_. eg. Human PAR on Y (default: exclude)
-seq_region_name Chromosome name if running a single seq_region
-write Specify if results should be written to the database
-verbose Increase verbosity of output messages
-log Dump decision matrices into a log file for analysis
CoreForeignKeys healthcheck:
./run-healthcheck.sh -d dbname -output problem CoreForeignKeys
A warning about not using CCDS is perfectly acceptible when not
running on Human, Mouse and Zebrafish.
EOS
;
}
Undocumented method
Code:
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sub usage {
print << "EOF";
perl test_code_from_html.pl
This script will strip and create seperate perl files for any block in the html
that is in surrounded by <pre class="code"> ... </pre>
The script adds registry code etc at the start if is not a full code example.
code as successfully executed.
-path The path to the ensembl-webcode directory (Must be set)
-user User name to be used for the mysql instance
-host Host name of the mysql instance (defualt ens-staging)
i.e. perl test_code_from_html -path ~/src
EOF
}
Undocumented method
Code:
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sub usage {
print << "EOF";
fingerprint_db.pl -user {user} -pass {password} -host {host} -port {port} -dbname {database} -tables {tables} -limit {rows}
Generates an MD5 checksum for the description and data of all or some tables of a database.
Argument to tables may be comma-separated, or multiple -tables arguments may be used.
If no -tables argument is given all tables are analysed.
Use -limit to limit the number of rows the comparison is based on; less accurate but faster for large tables.
A single fingerprint for the whole database can be computed by piping the output of this script into md5sum.
EOF
}
Undocumented method
Code:
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sub usage {
print STDERR <<EOF
Usage: kill_process_by_db options
Where options are: -host hostname
-user username
-pass password
-port port_of_server optional
-dbpattern regular expression that the database name has to match
EOF
;
exit;
}
Undocumented method
Code:
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sub usage {
print STDERR <<EOF
Usage: multidb_sql options
Where options are: -host hostname
-user username
-pass password
-port port_of_server optional
-dbpattern regular expression that the database name has to match
-expr sql statement you want to execute.
if omitted, just print database names matching
if select, show or describe prints results
-file Apply sql in file to all databases. Does not print results.
-result_only only prints out databases for which results where found
EOF
;
exit;
}
Undocumented method
Code:
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sub usage {
print << "EOF";
Finds all potential frameshifts (exons 1, 2 4 or 5 bp apart) in a database
and adds transcript attributes for them. Attribute value is intron length.
perl $0 {options}
Options ([..] indicates optional):
--host The database server to connect to.
[--port] The port to use. Defaults to 3306.
--user Database username. Must allow writing.
--pass Password for user.
--dbpattern Regular expression to define which databases are affected.
[--nostore] Don't store the attributes, just print results.
[--nodelete] Don't delete any existing "Frameshift" attributes before creating new ones.
[--print] Print transcript stable ID, intron number and length.
[--help] This text.
EOF
exit(0);
}
Undocumented method
Code:
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sub usage {
print <<USAGE_END;
USAGE:
generate_stable_ids.pl -dbuser|user {user}
-dbpass|pass {password}
-dbhost|host {host}
-dbport|port {port}
-dbname {database}
-types {gene,exon,transcript,translation}
-start {first stable ID}
Argument to -types is a comma-separated list of types of stable IDs to
be produced.
If the -types argument is ommitted, stable IDs are generated for all
types (gene,transcript,translation,exon).
Assigns stable IDs to objects that currently have none. The starting
stable ID is found by incrementing the highest current stable ID for
that type *or* by using -start argument. If no -start option is used
the script tries to find the latest given stable_id for each object
by looking up the <OBJ>_stable_id tables in the database and the
exon stable IDs!)
Please note that this script only works for "ENS..."-type stable ids.
It does not work for LRG ids or other types of stable ids.
Note:
The -start option requires to not submit an initial stable ID without
any gene, transcript, translation or exon specifier, as in
ENSMUS000001 (not ENSMUSG0001, then you end up with stable IDs like
ENSMUSGG001, ENSMUSGT0001.)
Again, the parameter to -start should be the stable ID you wish
to start from without the gene, transcript, translation or exon
specifier.
Examples:
- to generate only exon stable IDs starting with 223 for mouse, use
-start ENSMUS222 -types exon
- to generate exon and gene stable IDs, starting with 223 for mouse,
use
-start ENSMUS222 -types exon,gene
- to generate all types of stable IDs for human, which all start
with ID 666 use
-start ENS665
- to generate a whole new set of stable_ids (exon, transcript,
translation, gene) starting with 1 for an organism with prefix
ENSNEW you can use one of the following options :
-start ENSNEW0 <or>
-start ENSNEW0 <or>
-start ENSNEW00000000
The script produces SQL which can be run against the target database.
USAGE_END
} ## end sub usage
Undocumented method
Code:
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sub usage {
my $indent = ' ' x length($0);
print << 'EOF'; exit(0);
The script populates the CORE db's protein_feature table with all the uniprot mappings found in GIFTS db's ensp_u_cigar table.
Options -gfhost -gfport -gfuser -gfpass -gfdb are mandatory and specify the credentials for the server on which a GIFTS database exists
Options -pfhost -pfport -pfuser -pfpass -pfdb are credentials of the core db where the GIFTS data will be copied into
cd ensembl/misc-scripts/gifts_import/
eg:
(with -dryrun flag won't insert)
perl populate_protein_feature.pl -gfhost localhost -gfport 3306 -gfuser prem -gfpass prem -gfdb carlos_ensembl_gifts -pfhost localhost -pfport 3306 -pfuser prem -pfpass prem -pfdb homo_sapiens_core_91_38 -dryrun
(without -dryrun flag creates a full version)
perl populate_protein_feature.pl -gfhost localhost -gfport 3306 -gfuser prem -gfpass prem -gfdb carlos_ensembl_gifts -pfhost localhost -pfport 3306 -pfuser prem -pfpass prem -pfdb homo_sapiens_core_91_38
Usage:
$0 -gfhost giftsdb_host -gfport giftsdb_port -gfuser giftsdb_user -gfpass giftsdb_pass -gfdb giftsdb_dbname -pfhost protfeatdb_host -pfport protfeatdb_port -pfuser protfeatdb_user -pfpass protfeatdb_pass -pfdb protfeatdb_dbname
$indent [-help]
-gfhost GIFTS database host
-gfport GIFTS database port
-gfuser GIFTS database user
-gfpass GIFTS database password
-gfdb GIFTS database name
-pfhost core database host
-pfport core database port
-pfuser core database user
-pfpass core database pass
-pfdb core database name
-limit limit the number of rows to inserts - used only while testing
-dryrun dryrun, no insert
-help This message
EOF
}
Undocumented method
Code:
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sub usage {
print "Launching instructions:
Run from a folder you are happy to have filled with files.
Description:
Import data from a BED file into the simple_feature table. Only supports
6 column BED files (location, name and score).
Synopsis:
perl import_bed_simple_feature.pl -file [PATH} -db_name NAME
Undocumented method
Code:
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sub usage {
print "Launching instructions:
Run from a folder you are happy to have filled with files.
Options:
-url Supply the URL to download from
-db_name The DB to add these features to
-db_host Hostname for the DB
-db_user
-db_pass
-db_port
-db_version
-species
-help
";
}
Undocumented method
Code:
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sub usage {
print "Description:
A program for writing karyotype ranks into a core-like database. If one is
not specified then we query NCBI's assembly report resource for a candidate
list. The program also allows you to specify a custom rank if required.
This module uses LWP to communicate with NCBI's FTP site. Should you have
any issues please consult its documentation on how to debug the issue. Also
make sure you can access $NCBI_BASE
Synopsis:
perl karyotype_rank_assigner.pl -db_name NAME -db_host HOST -db_user USR -db_pass PASS -species human -group GRP
Options:
-db_name The DB to add the rank to
-database
-dbname
-db_host Hostname for the DB
-host
-dbhost
-db_user Username for the DB
-user
-username
-dbuser
-db_pass Password for the DB
-pass
-password
-dbpass
-db_port Port for the DB
-dbport
-port
-species Name of the species; defaults to human
-group Name of the DB group; defaults to core
-karyotype Comma separated list of karyotypes to write. Also
supports specifying this option multiple times
-no_interactive Do not prompt for confirmation
-help Print this message
";
}
Undocumented method
Code:
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sub usage {
print "Description:
Sort a feature table by seq_region_id, seq_region_start. Also run optimise
if specified. Holds a backup of the table that has just been sorted
unless told otherwise.
Synopsis:
perl sort_feature_table.pl -db_name NAME
Options:
-db_name The DB to add these features to
-database
-dbname
-db_host Hostname for the DB
-host
-dbhost
-db_user Username for the DB
-user
-username
-dbuser
-db_pass Password for the DB
-pass
-password
-dbpass
-db_port Port for the DB
-dbport
-port
-table The table(s) to sort. Specify multiple parameters
-tables
-optimise Optimise the table post sort
-nobackup Do not backup the original table
-nolock Stop the code from applying for table locks
-columns Specify the columns to sort on. Defaults to
seq_region_id, seq_region_start and seq_region_end.
Multiple parameters allowed
-help
";
}
Undocumented method
Code:
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sub usage{
print << "EOH";
This perl script will download (rsync) the necesary ftp files and load them into a new local
ensembl mysql database. It will check that the checksums match and do all the zipping and
unzipping of the files.
load_database_from_ftp.pl -root {root} -database {database} -new_database {database2}
-force -cleanup -quiet -help
-host {host} -port {port} -user {user} -pass {password}
-mysqltempdir {dir}
-root Root directory for ftp files
-database Database name to get data for
-new_database Name of the new database
-user User name to access database. Must allow writing.
-pass Password for user.
-host Database host.
-port Database port.
-force import data even if the checksums do not match
-cleanup remove the downloaded files at the end
-quiet No output except for serous error message
-mysqltmpdir Mysql may not have enough tmp space so this can be set to another directory
-help print this help text
examples:-
1) perl load_database_from_ftp_site.pl -database homo_sapiens_core_54_36p -host mysqlhostname
-user mysqluser -pass mysqlpassword -force
This will download the ftp files for the 54 release of the human core database and create a database
called <userid>_homo_sapiens_core_59_36p where userid is the login name of the user. To choose you
own database name use the -new_database option.
2) load_database_from_ftp_site.pl -databases homo_sapiens_core_57_37d -new_database homo_sapiens_core_59_37d
-host mysqlhostname -user mysqluser -pass mysqlpassword -quiet -cleanup -mysqltmpdir /scratch/
Will load the human core database into the mysql instance on mysqlhostname and use the directory
/scratch/ to use as the tmp directory for mysql.
EOH
}
Undocumented method
Code:
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sub usage{
print << "EOH";
It uses the Registry from the core API to get the species name to pass on to the script
load_database_from_ftp.pl.
load_multiple_databases.pl -root {root} -prefix {prefix} -release {number}
-species {s1,s2,s3} -groups {type1,type2} -force -cleanup -quiet -help
-host {host} -port {port} -user {user} -pass {password}
-mysqltempdir {dir} -list
-root Root directory for ftp files
-prefix Database name to get data for
-release Release version of the dtaabase to get
-species Comma separated list of species to get
-groups Comma separated list of database types to get
( from core,variation,funcgen,otherfeatures,vega etc or all)
-user User name to access database. Must allow writing.
-pass Password for user.
-host Database host.
-port Database port.
-force import data even if the checksums do not match
or the new database already exists.
-cleanup remove the downloaded files at the end
-quiet No output except for serous error message
-mysqltmpdir Mysql may not have enough tmp space so this can be set to another directory
-run If set will start the download etc else it will just list the databases.
NOTE: Not default as this script does alot so we want to make sure everything
is correct first before starting.
-help print this help text
examples:-
1) perl load_multiple_databases.pl -release 54 -groups core -species human -host mysqlhostname
-user mysqluser -pass mysqlpassword -force -run -prefix "copy_"
This will download the ftp files for the 54 release of the human core database and create a database
called copy_homo_sapiens_core_59_36p.
2) perl load_multiple_databases.pl -release 59 -species mouse -groups all -run
-host mysqlhostname -user mysqluser -pass mysqlpassword -quiet -cleanup -mysqltmpdir /scratch/
Will load the mouse databases for release 59 into the mysql instance on mysqlhostname and use the directory
/scratch/ to use as the tmp directory for mysql.
This will load the databases:-
mus_musculus_cdna_59_37l
mus_musculus_core_59_37l
mus_musculus_funcgen_59_37l
mus_musculus_otherfeatures_59_37l
mus_musculus_variation_59_37l
mus_musculus_vega_59_37l
EOH
}
Undocumented method
Code:
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sub usage {
print <<USAGE_END;
USAGE:
$0 --dbhost=ens-staging1 [--dbport=3306] \\
\t--dbuser=ensadmin --dbpass=XXX \\
\t--dbpattern=core
$0 --help
--dbpattern Specifies a regular expression for (possibly) matching
multiple databases.
--nobackup Do not backup the meta_coord table in a file.
--help Displays this help text.
This script will dump the current meta_coord table to a backup file in
the current directory. Then it will update the meta_coord table for the
data in the following tables:
USAGE_END
print( "\t", join( "\n\t", @table_names ), "\n" );
}
Undocumented method
Code:
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sub usage {
print <<EOF; exit(0);
Populate meta table with (e.g.) genebuild.level = toplevel if all genes
are top level. Using v41 API code this can speed fetching and dumping
greatly.
Usage: perl $0 <options>
--host|dbhost Database host to connect to.
--port|dbport Database port to connect to (default is 3306).
--dbpattern Database name regexp
--user|dbuser Database username.
--pass|dbpass Password for user.
--print Just print, don't insert or delete keys.
--help This message.
--verbose Prints out the name of the database
which is going to be patched.
If you like to patch just a single database you can also use this
command line :
perl meta_levels.pl --host ... --user ... --pass ... --port ... --dbname ...
EOF
} ## end sub usage
Arg [] : None Returntype : None Example :
Description : Print script usage string Exceptions : None Caller : General
Code:
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sub usage {
my $prog = `basename $0`; chomp($prog);
print "Usage: $prog [OPTIONS]\n\n";
print "Options:\n";
print " -ue Ping Ensembl US mirror\n";
print " -eg Ping Ensembl Genomes (can't be used together with \"ue\")\n";
print " -species <species> Use species <species> (use double quotes if species name contains spaces)\n";
print " -db_version <version> Use the specified version of Ensembl not the API version\n";
print " -grch37 Use human assembly GRCh37 rather than the default GRCh38 version\n";
print " -verbose Ping output is more verbose. Not recommended for Ensembl genomes\n";
print " -help Print this message\n";
print "\n\n";
exit 1;
}
Undocumented method
Code:
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sub usage {
print STDERR <<EOF
This program classifies the repeats stored in a core database into some
somewhat sensible categories. It does this through a combination of a
repeat.txt file extracted from RepeatMasker repeat libraries and through
some simple pattern matching of the repeat names.
usage: perl repeat-libraries.pl [-user <user>] [-port <port>] [-pass <pass>]
-host <host> -dbpattern <regexp> -repeatfile <file>
example: perl repeat-libraries.pl -user ensadmin -pass secret -host ecs1g \\
-dbpattern '^homo_sapiens_(core|vega)_20_34c$' -repeatfile repeats.txt
EOF
;
exit;
}
Undocumented method
Code:
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sub usage {
print STDERR <<EOF
This program classifies the repeats stored in a core database into some
somewhat sensible categories. It does this through a combination of a
repeat.txt file extracted from RepeatMasker repeat libraries and through
some simple pattern matching of the repeat names.
usage: perl repeat-types.pl [-user <user>] [-port <port>] [-pass <pass>]
-host <host> -dbpattern <regexp>
example: perl repeat-types.pl -user ensadmin -pass secret -host ecs1g \\
-port 3306 -dbpattern '^homo_sapiens_(core|vega)_20_34c$'
EOF
;
exit;
}
Undocumented method
Code:
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sub usage {
print STDERR <<EOC
Usage: perl shrink_trfs.pl -user .. -port .. -pass .. -host .. -dbname ..
Tries to minimize the number of repeat_consensi by only having one
trf consensus for each length of repeat_consensus longer than 8.
Shorter repeat consensi are reduced to the alphabetical minimum
of all rotate / revcomp equivalent repeats.
EOC
;
exit;
}
Undocumented method
Code:
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sub usage {
my $indent = ' ' x length($0);
print <<USAGE_END;
Usage:
$0 --host=dbhost [ --port=dbport ] \\
$indent --user=dbuser [ --pass=dbpass ] \\
$indent --type=schema-type | --database=dbname \\
$indent [ --release=new-release ] [ --from=old-release ] \\
$indent [ --species=dbspecies ] \\
$indent [ --gitdir=/some/path ] \\
$indent [ --dryrun ] \\
$indent [ --interactive 0|1 ]\\
$indent [ --verbose ] [ --quiet ] \\
$indent [ --mysql=optional_path ] \\
$indent [ --fix ] \\
$indent [ --fixlast ]
$0 --help | --about
$0 --version
--host / -h\tdatabase host name (required)
--port / -P\tdatabase port (optional, default=3306)
--user / -u\tdatabase user (required)
--pass / -p\tdatabase user password (optional, no default)
--type / -t restrict to database schema type
(i.e. core, compara, funcgen, gene2phenotype, variation, production or ontology)
(required if --database is not specified)
--database / -d full name of database, or database name pattern
(required if --type is not specified)
--release / -r release number (optional, default is the latest
release that we can find patches for)
--from / -f only consider databases from this release
(optional, no default)
--species / -s restrict to species (optional, no default)
--gitdir the directory where the relevant Ensembl Git repositories
have been checked out (optional, default=misc-scripts/../..)
--dryrun / -n do not actually modify databases
(optional, default=not set)
--verbose / -v display extra information
--quiet / -q do not display warnings
--fix also go through all old patches to find any missing
patch (patching starts at release equal to the
oldest patch in the database) >>USE WITH CAUTION<<
--oldest used in conjunction with --fix, this option allows control
over how many releases are included in the fix. This option
exists for users who have incomplete meta entries and
wish to bring their database automatically up to date.
--fixlast an extension of B<--oldest> and B<--fix>. This combines
to patch the current and last release only, giving an easy
way to patch a database post-handover without worrying
about ancient patches.
--mysql specify the location of the mysql binary if it is not on
\$PATH. Otherwise we default this to mysql
--nointeractive specify if you want an non-interactive patching environment
(default false). >>USE WITH CAUTION<<
--help display this text
--about display further information
--version display version and quit
USAGE_END
} ## end sub usage
Undocumented method
Code:
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sub usage {
my $indent = ' ' x length($0);
print <<EOF; exit(0);
The script populates a stable_id lookup database with all stable ids found in databases
on a specified server for a specified db release.
Stable ids are copied for objects listed in hash %group_objects
The script is used for both ensembl and ensembl genomes
Options -lhost -lport -luser -lpass -version are mandatory and specify the credentials for the server on which a stable id lookup database exists or is to be created (if using option -create).
If an argument for option -ldbname is not provided, the default name for the database wil be used: 'ensemblgenomes_stable_id_lookup_xx', where xx is the database release (option -version).
Options -host -user -port specify the credentials of the server(s) where stable ids are to be copied from.
To run the script cd into the directory where the script lives eg:
cd ensembl/misc-scripts/stable_id_lookup/
This command will create database ensembl_stable_ids_88 on server mysql-xxx-dev.ebi.ac.uk for release 88 databases found on mysql-ens-xxx.ebi.ac.uk:
eg:
(with -test flag create a small subset database)
perl populate_stable_id_lookup.pl -lhost mysql-xxx-dev.ebi.ac.uk -luser xxxrw -lpass xxxx -lport 4484 -dbname ensembl_stable_ids_88 -create -host mysql-ens-xxx.ebi.ac.uk -user ensro -port 4519 -version 88 -test
(without -test flag creates a full version)
perl populate_stable_id_lookup.pl -lhost mysql-xxx-dev.ebi.ac.uk -luser xxxrw -lpass xxxx -lport 4484 -dbname ensembl_stable_ids_88 -create -host mysql-ens-xxx.ebi.ac.uk -user ensro -port 4519 -version 88
Usage:
$0 -lhost host_name -lport port_number -luser user_name -lpass password -version db_version
$indent [-create] [-dbname database_name]
$indent [-help]
-h|host Database host where stable_ids are to be copied from (multiple hosts can be specified)
-u|user Database user where stable_ids are to be copied from (each host needs a user specified,
if multiple -h|host options are given and fewer -u|user options are specified,
the first user name will be used for the hosts where no user name was given)
-port Database port where stable_ids are to be copied from (if more than one host is specified
multiple ports can be provided)
-lh|lhost Database host where stable_id lookup database exists or is to be created
-lu|luser Database user where stable_id lookup database exists or is to be created
-lp|lpass Database password where stable_id lookup database exists or is to be created
-lport Database port where stable_id lookup database exists or is to be created
-v|version EG version to match, e.g 88_77 OR Ensembl version to match 88
-db|dbname Database name for the stable id lookup database, e.g ensembl_stable_ids_88
-create Create the stable id lookup database using sql source ./sql/tables.sql
-help This message
EOF
}
Undocumented method
Code:
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sub usage {
my $msg = shift;
print STDERR "$msg\n\n" if($msg);
print STDERR <<EOF;
usage: perl convert_seqstore <options>
options: -file <input_file> input file with tab delimited 'species',
'host', 'source_db', 'target_db' values
on each line
-schema <table_file> file containing SQL schema definition
-vega_schema <table_file> file containing SQL for additional Vega tables
-user <user> a mysql db user with read/write priveleges
-password <password> the mysql user's password
-verbose print out debug statements
-force replace any target dbs that already exists
-limit <num_rows> limit the number of features transfered to
speed up testing
-help display this message
example: perl convert_seqstore.pl -file converter.input \\
-schema ../../sql/table.sql -user ensadmin -password secret \\
-force -verbose
EOF
#'
exit;
}
Undocumented method
Code:
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sub usage {
print STDERR
qq{
This program will convert the coordinates of alignment features from
their current cooridinate systems to coordinates on toplevel sequence
regions. This can speed up the retrieval of these features dramatically.
Features which are partially or entirely non-golden portions of
sequence regions will be discarded.
This program is only capable of mapping if there is a direct relationship
between the coordinate systems defined in the assembly and meta tables.
This program can use a different database to obtain the assembly information
but the database must be on the same MySQL instance. This is useful for
satellite databases such as the est database.
usage:
perl push_align_features -dbname <dbname> -user <user> -host <host> \
[-port <port>] [-pass <pass>] [-dnadbname <dbname>]
};
exit;
}
Undocumented method
Code:
click to view
sub usage {
print STDERR qq {
This program merges exons which are seperated by introns of length 1 or 2
and replaces them with a frameshift mrna edit.
Usage:
perl shortintrons2frameshift.pl -user <user> -host <host> [-pass <password>] \
-dbname <dbname> [-port <port>]
};
exit;
}
Undocumented method
Code:
click to view
sub usage {
print<<EOF;
Transfer karyotype data from old to new database, scaling appropriately.
perl transfer_karyotype.pl -oldhost ... -olduser ... -oldpass ... -oldport ... -olddbname ... -newhost ... -newuser ... -newpass ... -newport ... -newdbname
EOF
exit(1);
}
Undocumented method
Code:
click to view
sub usage {
my $indent = ' ' x length($0);
print <<EOF; exit(0);
The script populates a stable_id lookup database with all stable ids found in databases
on a specified server (or servers) for a specified db release.
Stable ids are copied for objects listed in hash %group_objects
Options -lhost -luser -lpass are mandatory and specify the credentials for the server on which a stable id lookup database exists or is to be created (if using option -create). If an argument for option -ldbname is not provided, the default name for the database wil be used: 'ensembl_stable_id_lookup_xx', where xx is the database release (option -db_version).
Options -host -user -port specify the credentials of the server(s) where stable ids are to be copied from.
To run the script cd into the directory where the script lives eg:
cd ensembl/misc-scripts/stable_id_lookup/
This command will create database ensembl_stable_id_lookup_67 on server ens-staging1 and will copy stable ids from databases for release 67 found on ens-staging1 and ens-staging2:
populate_stable_id_lookup.pl -lhost ens-staging1 -luser ensadmin -lpass xxxx -create -db_version 67 -host ens-staging1 -host ens-staging2 -user ensro
Usage:
$0 -xhost host_name -xuser user_name -xpass password
$indent [-xport port_number]
$indent -host host_name -user user_name
$indent [-port port_number] [-db_version]
$indent -species species_name
$indent [-dontdrop]
$indent [-help]
-h|host Database host where the species db lives
-u|user Database user where the species db lives
-port Database port the species db lives
-xh|xhost Database host where the xref mindmap db is to be created
-xu|xuser Database user where the xref mindmap db is to be created
-xp|xpass Database password where the xref mindmap db is to be created
-xport Database port where the xref mindmap db is to be created
-s|species Species name to generate xref mindmap for
-d|dontdrop Don\'t drop the xref_mindmap db at the end of the script
-db_version If not specified, software_version() returned by the ApiVersion module will be used
-help This message
EOF
}
Undocumented method
Code:
click to view
sub usage {
print << "EOF";
xref_parser.pl -host {host} -port {port} -user {user} -pass {pass} -dbname {dbname} -release {release} \\
-species {species} -taxon_id {taxon_id} \\
-parser {parser} -source {source_id} -file {file} \\
-db {db} =keep_db {keep_db} \\
-help
-user User name to access database. Must allow writing.
-pass Password for user.
-host Database host.
-port Database port.
-dbname Name of xref database to use/create.
-release Release version of the species to parse
Used to find the right database on the server specified in the arguments
-species Which species to import.
Species may be referred to by genus/species
(e.g. homo_sapiens) or common aliases (e.g. human).
Specifying an unknown species will cause a list
of valid species to be printed.
-taxon Which taxon to import.
Can be used as an alternative to species.
-division Which division the species belongs to.
This defines which sources will be parsed and does
not necessarily imply taxonomic relationship
(e.g. ciona intestinalis is a vertebrate in this context)
-parser Which parser to run
-source Name of the source to extra data for (should match equivalent parser)
-file Location and name of the file to be parsed
Path should be absolute
-db If the parser requires connection to a database, specify here
For example, specify otherfeatures when running RefSeqCoordinateParser
-keep_db When re-using an existing xref database, use the option
By default, deletes any existing one and creates a new one
EOF
}
Undocumented method
Code:
click to view
sub usage {
print <<EOT;
Usage:
\t$0 [-date <day_of_the_patch>] [-driver <name_of_first_driver>] [-driver <name_of_second_driver>] ...
\t$0 -h
\t-date\n\t\tdate in ISO format, e.g. 2015-02-14. Defaults to the current date
\t-driver (can be repeated)\n\t\tdriver for which create a patch. Defaults to MySQL, SQLite, and Postgre
\t-h|--help\n\t\tdisplay this help text
EOT
}
Undocumented method
Code:
click to view
sub usage {
print q{
Usage: perl sql2html.pl [OPTION]
Convert the SQL documentation into an HTML document.
Options:
-help Print this message
-help_format Print the description of the documentation format in the SQL files
An input file must be specified. This file must be a SQL file, with the "Java-doc like documentation".
For more information, please visit the following page:
http://www.ebi.ac.uk/seqdb/confluence/display/EV/SQL+documentation
-i A SQL file name (Required)
-fk An external SQL file name with foreign keys statements (Optional)
-o An HTML output file name (Required)
-d The name of the database (e.g Core, Variation, Functional Genomics, ...)
-c A flag to display the colours associated with the tables (1) or not (0). By default, the value is set to 1.
-v Version of the schema. Replace the string ####DB_VERSION#### by the value of the parameter "-v", in the introduction text. (Optional)
-intro A html/text file to include in the Introduction section (Optional. If not provided a default text will be inserted)
-html_head A html/text file to include extra text inside the html <head></head> tags. (Optional)
-show_header A flag to display headers for a group of tables (1) or not (0). By default, the value is set to 1.
-embed_diagrams A flag to include schema diagrams as dot graphs
-sort_headers A flag to sort (1) or not (0) the headers by alphabetic order. By default, the value is set to 1.
-sort_tables A flag to sort (1) or not (0) the tables by alphabetic order. By default, the value is set to 1.
Other optional options:
# If you want to add some SQL query results as examples:
-url URL of the database that has some data
-skip_connection Avoid to run the MySQL queries contained in the "@example" tags.
} . "\n";
exit(0);
}
