get_embl_entry

Biopiece: get_embl_entry

Description

get_embl_entry lookup EMBL entries in a MySQL database and flatfiles from ids given in the stream as ID keys or using the -i switch. The output is parsed into Biopieces records. Per default all of the EMBL record is parsed, but this can be limited using the ´-k´, ´-f´, and ´-q´ switches.

For parsing EMBL files direcly use read_embl.

See how to setup default MySQL username and password here: http://code.google.com/p/biopieces/wiki/HowTo#Howto_setup_default_MySQL_username_and_password

Usage

... | get_embl_entry [options]

Options

[-?          | --help]               #  Print full usage description.
[-u <string> | --user=<string>]      #  MySQL user                                 -  Default=<from ~/.biopiecesrc>
[-p <string> | --password=<string>]  #  MySQL user password                        -  Default=<from ~/.biopiecesrc>
[-d <string> | --database=<string>]  #  MySQL database                             -  Default=<from ~/.biopiecesrc>
[-t <string> | --table=<string>]     #  MySQL table to create                      -  Default=<from ~/.biopiecesrc>
[-i <list>   | --ids=<list>]         #  Comma seperated list of ids to get.
[-k <list>   | --keys=<list>]        #  Comma seperated list of keys to get        -  Default=all
[-f <list>   | --features=<list>]    #  Comma seperated list of features to get    -  Default=all
[-q <list>   | --qualifiers=<list>]  #  Comma seperated list of qualifiers to get  -  Default=all
[-I <file!>  | --stream_in=<file!>]  #  Read input from stream file                -  Default=STDIN
[-O <file>   | --stream_out=<file>]  #  Write output to stream file                -  Default=STDOUT
[-v          | --verbose]            #  Verbose output.

Examples

See read_embl for examples on how to modify the parsing of EMBL records.

To obtain all EMBL records from Biopiece records in the stream, where the key ID holds the EMBL ID as value, simply do:

... | embl_get_entry

or so specify EMBL IDs using the -i switch:

get_embl_entry -i DS179687

See also

read_embl

read_mysql

write_mysql

list_mysql_databases

remove_mysql_tables

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

July 2009

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

get_embl_entry is part of the Biopieces framework.

http://www.biopieces.org