EMBOSS FAQ (Frequently Asked Questions)

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  EGC.0
  EGC.1
  EGC.2
  EGC.3
  EGC.4
  EGC.5
  EGC.6
  EGC.9
  EGC.10
  EGC.12
  EGC.11
  EGC.13
  EGC.14
  EGC.15

These files are the only ones that you can specify to 'transeq'.

If you wish to create your own specialised translation table, then you should pick one of them to amend.

For instance you may decide that you will use the file EGC.15 as you would never want to use this otherwise.

Use the program 'embossdata' to get a copy of this file:

% embossdata -fetch -filename EGC.15
Finds or fetches the data files read in by the EMBOSS programs
File '/packages/emboss/emboss/data/EGC.15' has been copied successfully.

Edit the file EGC.15 to suit your requirements.

Specify '-table 15' when you run 'transeq' to use this altered file. 'transeq' will then look for the file 'EGC.15' and will find it in your current directory before it finds the default one in the EMBOSS_DATA directory. It will therefore use your local copy.

You may get confused with many copies of changed files floating about. To check which copy of a file is being used - the default EMBOSS_DATA one or a potential local copy, use 'embossdata':

% embossdata -filename EGC.15
Finds or fetches the data files read in by the EMBOSS programs
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.

File ./EGC.15                                            Exists
File .embossdata/EGC.15                                  Does not exist
File /people/gwilliam/EGC.15                             Does not exist
File /people/gwilliam/.embossdata/EGC.15                 Does not exist
File /packages/emboss/emboss/data/EGC.15                 Exists

This shows that a copy of EGC.15 exists in your current directory and so will be used in preference to the default one in the EMBOSS_DATA directory.

SECTION E - Sequence Files and Formats

Q) How do you write sequences to different files instead of writing them all to one file?

You should consider using the '-ossingle' qualifier. This writes sequences to separate FASTA files, but the file names depend on the sequence ID. This is rarely used. It is there because -ossingle is the default for GCG output format. The output filename is currently ignored when ossingle is used, and the filename depends on each individual sequence.

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