EMBOSS: yank

| ## EMBOSS: yank

# Program yank

## Function

Reads a sequence range, appends the full USA to a list file

## 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.

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:

- opsd_abyko.fasta - this is the name of a sequence file. The file is read in from the current directory.
- sw:opsd_xenla - this is a reference to a specific sequence in the SwissProt database
- sw:opsd_c* - this represents all the sequences in SwissProt whose identifiers start with ``opsd_c''
- another_list - this is the name of a second list file

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.

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.

## Usage

Here is a sample session with yank, adding the regions making up the coding sequence of embl:hsfau1 to the list 'cds.list':

    % yank
    Reads a range from a sequence, appends the full USA to a list file
    Input sequence: em:hsfau1
         Begin at position [start]: 782
           End at position [end]: 856
            Reverse strand [N]:
    Output file [hsfau1.yank]: cds.list

    % yank
    Reads a range from a sequence, appends the full USA to a list file
    Input sequence: em:hsfau1
         Begin at position [start]: 951
           End at position [end]: 1095
            Reverse strand [N]:
    Output file [hsfau1.yank]: cds.list

    % yank
    Reads a range from a sequence, appends the full USA to a list file
    Input sequence: em:hsfau1
         Begin at position [start]: 1557
           End at position [end]: 1612
            Reverse strand [N]:
    Output file [hsfau1.yank]: cds.list

    % yank
    Reads a range from a sequence, appends the full USA to a list file
    Input sequence: em:hsfau1
         Begin at position [start]: 1787
           End at position [end]: 1912
            Reverse strand [N]:
    Output file [hsfau1.yank]: cds.list

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          sequence   Sequence USA
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -newfile            bool       Overwrite existing output file

       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
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.yank
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-newfile | Overwrite existing output file | Yes/No | No

## Input file format

Any valid sequence can be read in.

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 result file 'cds.list' of the example above is:

    em-id:HSFAU1[782:856]
    em-id:HSFAU1[951:1095]
    em-id:HSFAU1[1557:1612]
    em-id:HSFAU1[1787:1912]

This 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.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
splitter | Split a sequence into (overlapping) smaller sequences
swissparse | Retrieves sequences from swissprot using keyword search
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences

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

## Author(s)

This application was written by Peter Rice (peter.rice@uk.lionbioscience.com)

## History

Written (March 2002) - Peter Rice.

## Target users

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

## Comments