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get_embl_entry
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
... | get_embl_entry [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.
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
Martin Asser Hansen - Copyright (C) - All rights reserved.
July 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
get_embl_entry is part of the Biopieces framework.