yank

Function

Description

yank is a simple utility to add a specified sequence name to a list file.

In fact, it writes out not just the name of the sequence, but also the start and end position of a region within that sequence and, if the sequence is nucleic, if can specify whether the sequence is the reverse complement.

Without the program yank you would need to use a text editor such as pico to create the appropriate list files. yank makes this process easy.

List Files

Many EMBOSS programs can read in a set of sequences. (Some examples are emma and union) There are many ways of specifying these sequences, including wildcarded sequence file names, wildcarded database entry names and list files. List files (files of file names) are the most flexible. yank is a utility to add sequences to a list file.

Instead of containing the sequences themselves, a List file contains "references" to sequences - so, for example, you might include database entries, the names of files containing sequences, or even the names of other list files. For example, here's a valid list file, called seq.list:

unix % more seq.list 

opsd_abyko.fasta
sw:opsd_xenla
sw:opsd_c*
@another_list

This looks a bit odd, but it's really very straightforward; the file contains:

Notice the @ in front of the last entry. This is the way you tell EMBOSS that this file is a list file, not a regular sequence file.

Usage

Command line arguments


Input file format

yank reads any valid sequence USA.

You will be prompted for the start and end positions you wish to use.

If the sequence is nucleic, you will be prompted whether you wish to use the reverse complement of the sequence.

Output file format

The output list file can now be read in by a program such as union by specifying the list file as '@cds.list' when union prompts for input.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

The program extract does not make list files, but creates a sequence from sub-regions of a single other sequence.

Author(s)

History

Target users

Comments