EMBOSS: wordcount

| ## EMBOSS: wordcount

# Program wordcount

## Function

Counts words of a specified size in a DNA sequence

## Description

    Displays all the words of the specified length with the number of
    times it occurs.

## Usage

Here is a sample session with wordcount.

    % wordcount embl:rnu68037 -wordsize=3
    Counts words of a specified size in a DNA sequence
    Output file [rnu68037.wordcount]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
       -wordsize           integer    Word size
       -outfile            outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence USA | Readable sequence | Required
-wordsize | Word size | Integer 2 or more | 4
-outfile | Output file name | Output file | <sequence>.wordcount
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any sequence USA.

## Output file format

The output sequence produced in the above example is:

    ctg     54
    tgg     53
    gcc     53
    ggc     51
    cgc     47
    gct     47
    gtg     40
    tgc     39
    cct     38
    gcg     36
    cca     29
    ggg     26
    cag     25
    ctt     25
    tcc     25
    ggt     24
    ccc     24
    ctc     23
    tgt     23
    gca     22
    cgt     22
    ccg     22
    cac     22
    agc     21
    acg     19
    ttg     19
    cgg     19
    tcg     18
    ttc     17
    cat     17
    agg     17
    act     16
    gtc     16
    gag     16
    aac     15
    gga     14
    atc     14
    tct     14
    tca     13
    cta     13
    atg     12
    gtt     11
    acc     11
    gta     11
    aca     10
    tac     10
    tga     10
    caa     10
    gac     9
    agt     9
    tag     9
    ttt     8
    cga     7
    gat     6
    taa     6
    tat     5
    aga     5
    gaa     4
    aat     3
    ata     3
    tta     3
    att     3
    aag     2
    aaa     1

The file simply consists of two columns, separated by spaces or TAB characters.

The first column consists of all the possible words of size wordsize. The second column consists of the count of those words in the input sequence.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

0 if successful.

## Known bugs

None.

## See also

Program name | Description
--- | ---
banana | Bending and curvature plot in B-DNA
btwisted | Calculates the twisting in a B-DNA sequence
chaos | Create a chaos game representation plot for a sequence
compseq | Counts the composition of dimer/trimer/etc words in a sequence
dan | Calculates DNA RNA/DNA melting temperature
freak | Residue/base frequency table or plot
isochore | Plots isochores in large DNA sequences

## Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Completed 27th November 1998.

## Target users

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

## Comments