EMBOSS: newseq manual

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.
  [-description]       string     Enter any description of the sequence that
                                  you require.
  [-type]              menu       Type of sequence
  [-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.
  [-outseq]            seqout     Output sequence 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 deaths

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)

[-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)

Output sequence USA

Writeable sequence

<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          STANDARD;      PRT;    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.

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
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
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

Function

Description

Usage

Command line arguments

Input file format

Output file format

Output files for usage example

File: mycc.pep

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments