Module: rje_embl Description: RJE Module to Handle EMBL Nucleotide Files Version: 0.1 Last Edit: 20/11/08

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_sequence rje_uniprot

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module contains methods for handling EMBL Nucleotide files, primarily in other rje modules but also with some standalone functionality. It is built on rje_uniprot and a lot of the initial functionality is designed around converting EMBL files to be compatible with programs designed with UniProt files in mind.

This module can be used to extract a list of entries from a larger database and/or to produce summary tables from flat files.

Input Options

embldat=FILE : Name of EMBL file [None]
emblpath=PATH : Path to EMBL Datafile (will look here for DB Index file)
dbindex=FILE : Database index file [uniprot.index]
extract=LIST : Extract IDs/AccNums in list. LIST can be FILE or list of IDs/AccNums X,Y,.. []
acclist=LIST : As Extract.
specdat=LIST : Make a DAT file of the listed species from the index (over-rules extract=LIST) []

Output Options

makeindex=T/F : Generate UniProt index files [False]
makespec=T/F : Generate species table [False]
makefas=T/F : Generate fasta files [False]
datout=FILE : Name of new (reduced) DAT file of extracted sequences [None]
outformat=X : Format for generated DAT file (uniprot/embl) [embl]
splitout=PATH : If path given, will split output into individual files per entry into PATH []
tabout=FILE : Table of extracted details [None]
linkout=FILE : Table of extracted Database links [None]
ftout=FILE : Outputs table of features into FILE [None]

Format Conversion Options

ucft=X : Feature to add for UpperCase portions of sequence []
lcft=X : Feature to add for LowerCase portions of sequence []
maskft=LIST : List of Features to mask out []
invmask=T/F : Whether to invert the masking and only retain maskft features [False]
caseft=LIST : List of Features to make upper case with rest of sequence lower case []
ftskip=LIST : List of feature details to skip ['transl_table','translation']

General Options

append=T/F : Append to results files rather than overwrite [False]
memsaver=T/F : Memsaver option to save memory usage - does not retain entries in object [False]

History Module Version History

    # 0.0 - Initial Compilation modified from rje_uniprot.
    # 0.1 - Added type storage and file splitting during conversion.