prettyseq

Function

Description

This writes out a nicely formatted display of the sequence with the translation (within specified ranges) displayed beneath it.

The translated nucleic acid region will be shown in lower-case letters while the rest of the input sequence will be left in the input case.

The base and residue numbers of the sequences are shown beside the sequences in the output.

Slightly unusually, this application uses the codon usage tables to translate the codons.

Usage

Command line arguments


Input file format

prettyseq reads any nucleic acid sequence USA.

You can specifiy a file of ranges to extract by giving the '-range' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-range @myfile').

The format of the range file is:

An example range file is:


# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

Output file format

Data files

The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS' directory of the EMBOSS distribution. If the name of a codon usage file is specified on the command line, then this file will first be searched for in the current directory and then in the 'data/CODONS' directory of the EMBOSS distribution.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

"Range outside length of sequence" - this is self explanatory. You should specify a range of sequences to translate that is within the length of the input sequence.

Exit status

It always exits with a status of 0.

Known bugs

None.

showseq has more options for specifying various ways of displaying a sequence, with or without various ways of translating it.

Author(s)

History

Target users

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