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:
- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by
one or more space or TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the
line.
- White-space before or after the text is removed.
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
Comments