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EMBOSS: infobase
infobase

 

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

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Function

Return information on a given nucleotide base

Description

infobase reports the defined properties for all known bases, or for any bases specified by the user.

Usage

Here is a sample session with infobase 


% infobase 
Return information on a given nucleotide base
Nucleotide base code [ABCDGHKMNRSTUVWXY]: 
Output file [outfile.infobase]:

Go to the output files for this example

Command line arguments 

Return information on a given nucleotide base
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-code]              string     [ABCDGHKMNRSTUVWXY] Enter IUPAC nucleotide
                                  base codes, e.g. A, C, G, T, R, Y etc. (Any
                                  string)
  [-outfile]           outfile    [*.infobase] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-code]
(Parameter 1)		 string Enter IUPAC nucleotide base codes, e.g. A, C, G, T, R, Y etc. Any string ABCDGHKMNRSTUVWXY
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.infobase
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

infobase uses a string of base codes.

Output file format

infobase outputs a text table of base properties.

Output files for usage example

File: outfile.infobase

Code Ambiguity  Complement Mnemonic
A    A          T          adenine
B    CGT        V          not_adenine
C    C          G          cytosine
D    AGT        H          not_cytosine
G    G          C          guanine
H    ACT        D          not_guanine
K    GT         M          keto_base
M    AC         K          amino_base
N    ACGT       N          any_base
R    AG         Y          purine_base
S    CG         S          strong_bond
T    T          A          thymine
U    T          A          uracil
V    ACG        B          not_thymine/uracil
W    AT         W          weak_bond
X    ACGT       X          unknown
Y    CT         R          pyrimidine

Data files

infobase reads the Ebases.iub file to define IUB standard codes for nucleotides and ambiguity codes.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run: 

% embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run: 


% embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

  • . (your current directory)
  • .embossdata (under your current directory)
  • ~/ (your home directory)
  • ~/.embossdata

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
inforesidue Return information on a given amino acid residue

Author(s)

Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None