EMBOSS: newseq

| newseq

## Function

Type in a short new sequence

## Description

This allows you to type a sequence into a file in a quick and easy manner.

The length of the sequence you can type in is restricted to a fairly short length (typically less than 255 characters). This length restriction is not a property of the EMBOSS package, but of the computer system you are using. This is because, as you type in response to a prompt from this program, what you type is stored in the computer operating system before being handed over to the program. There is often a limit of less than 255 characters on the length of a response that a computer system will allow you to give.

Despite this restriction, it is expected that this program will be a useful and easy way of constructing new sequence files.

(You wouldn't want to type a long sequence in by hand, anyway, would you?)

## Usage

Here is a sample session with newseq

Type in a short sequence to the file 'mycc.pep' in SWISSPROT format:

    % newseq
    Type in a short new sequence.
    Name of the sequence: cytoc
    Description of the sequence: fragment of cytochrome c
    Type of sequence
             N : Nucleic
             P : Protein
    Type of sequence [N]: p
    Enter the sequence: KKKEERADLIAY
    output sequence [outfile.fasta]: swiss::mycc.pep

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-name]              string     The name of of the sequence should be a
                                      single word that you will use to identify
                                      the sequence. It should have no (or few)
                                      punctuation characters in it. (Any string is
                                      accepted)
      [-description]       string     Enter any description of the sequence that
                                      you require. (Any string is accepted)
      [-type]              menu       [N] Type of sequence (Values: N (Nucleic); P
                                      (Protein))
      [-sequence]          string     The sequence itself.
                                      Because of the limitation of the operating
                                      system, you will only be able to type in a
                                      short sequence of (typically) 250
                                      characters, or so.
                                      The keyboard will beep at you when you have
                                      reached this limit and you will not be able
                                      to press the RETURN/ENTER key until you have
                                      deleted a few characters. (Any string is
                                      accepted)
      [-outseq]            seqout     [.] Sequence filename and
                                      optional format (output USA)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-outseq" associated qualifiers
       -osformat5          string     Output seq format
       -osextension5       string     File name extension
       -osname5            string     Base file name
       -osdirectory5       string     Output directory
       -osdbname5          string     Database name to add
       -ossingle5          boolean    Separate file for each entry
       -oufo5              string     UFO features
       -offormat5          string     Features format
       -ofname5            string     Features file name
       -ofdirectory5       string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write standard output
       -filter             boolean    Read standard input, write standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-name] (Parameter 1) | The name of of the sequence should be a single word that you will use to identify the sequence. It should have no (or few) punctuation characters in it. | Any string is accepted | An empty string is accepted
[-description] (Parameter 2) | Enter any description of the sequence that you require. | Any string is accepted | An empty string is accepted
[-type] (Parameter 3) | Type of sequence |
N | (Nucleic)
P | (Protein)
| N
[-sequence] (Parameter 4) | The sequence itself. Because of the limitation of the operating system, you will only be able to type in a short sequence of (typically) 250 characters, or so. The keyboard will beep at you when you have reached this limit and you will not be able to press the RETURN/ENTER key until you have deleted a few characters. | Any string is accepted | An empty string is accepted
[-outseq] (Parameter 5) | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

## Output file format

newseq writes a normal sequence file.

### Output files for usage example

### File: mycc.pep

    ID   cytoc          Unreviewed;         12 AA.
    DE   fragment of cytochrome c
    SQ   SEQUENCE    12 AA;   1464 MW;  6F142FA88DADC40B CRC64;
         KKKEERADLI AY
    //

## Data files

None.

## Notes

The length of the sequence you can type in is restricted to a fairly short length (typically less than 255 characters). If your computer beeps at you, you will typically have to delete the last character you typed and press the RETURN key.

## 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
codcopy | Reads and writes a codon usage table
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
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
listor | Write a list file of the logical OR of two sets of sequences
makenucseq | Creates random nucleotide sequences
makeprotseq | Creates random protein sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
noreturn | Removes carriage return from ASCII files
notseq | Exclude a set of sequences and write 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
skipseq | Reads and writes (returns) sequences, skipping first few
splitter | Split a sequence into (overlapping) smaller sequences
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
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

Written (1999) - Gary Williams

## Target users

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

## Comments

None