newseq

 

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Function

Create a sequence file from a typed-in sequence

Description

newseq creates a sequence file from a sequence that is manually typed in at the command-line. This is a quicker, easier and less error-prone method than editing such a file in a text editor.

Usage

Here is a sample session with newseq

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


% newseq 
Create a sequence file from a typed-in 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

Create a sequence file from a typed-in sequence
Version: EMBOSS:6.5.0.0

   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)
  [-description]       string     Enter any description of the sequence that
                                  you require. (Any string)
  [-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)
  [-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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-name]
(Parameter 1)
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  
[-description]
(Parameter 2)
string Enter any description of the sequence that you require. Any string  
[-type]
(Parameter 3)
list Type of sequence
N (Nucleic)
P (Protein)
N
[-sequence]
(Parameter 4)
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  
[-outseq]
(Parameter 5)
seqout Sequence filename and optional format (output USA) Writeable sequence <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outseq" associated seqout qualifiers
-osformat5
-osformat_outseq
string Output seq format Any string  
-osextension5
-osextension_outseq
string File name extension Any string  
-osname5
-osname_outseq
string Base file name Any string  
-osdirectory5
-osdirectory_outseq
string Output directory Any string  
-osdbname5
-osdbname_outseq
string Database name to add Any string  
-ossingle5
-ossingle_outseq
boolean Separate file for each entry Boolean value Yes/No N
-oufo5
-oufo_outseq
string UFO features Any string  
-offormat5
-offormat_outseq
string Features format Any string  
-ofname5
-ofname_outseq
string Features file name Any string  
-ofdirectory5
-ofdirectory_outseq
string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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

There will be a maximum permissible length (typically 255 characters) of the sequence that may be entered. This is not a property of the EMBOSS package but of the computer system you are using. Whenever you type something in at the command-line, the text is stored in a buffer before being passed to the program. There is often a limit of less than 255 characters on the size of the buffer and so also the size of the sequence you can specify to newseq. The computer will normally issue a beep when the end of buffer is reached, and allow no more character input.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
aligncopy Read and write alignments
aligncopypair Read and write pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Remove a section from a sequence
degapseq Remove non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieve sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
extractfeat Extract features from sequence(s)
extractseq Extract regions from a sequence
featcopy Read and write a feature table
featmerge Merge two overlapping feature tables
featreport Read and write a feature table
feattext Return a feature table original text
listor Write a list file of the logical OR of two sets of sequences
makenucseq Create random nucleotide sequences
makeprotseq Create random protein sequences
maskambignuc Mask all ambiguity characters in nucleotide sequences with N
maskambigprot Mask all ambiguity characters in protein sequences with X
maskfeat Write a sequence with masked features
maskseq Write a sequence with masked regions
nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn Remove carriage return from ASCII files
nospace Remove whitespace from an ASCII text file
notab Replace tabs with spaces in an ASCII text file
notseq Write to file a subset of an input stream of sequences
nthseq Write to file a single sequence from an input stream of sequences
nthseqset Read and write (return) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Read and count sequences
seqret Read and write (return) sequences
seqretsetall Read and write (return) many sets of sequences
seqretsplit Read sequences and write them to individual files
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Read and write (return) sequences, skipping first few
splitsource Split sequence(s) into original source sequences
splitter Split sequence(s) into smaller sequences
trimest Remove poly-A tails from nucleotide sequences
trimseq Remove unwanted characters from start and end of sequence(s)
trimspace Remove extra whitespace from an ASCII text file
union Concatenate multiple sequences into a single sequence
vectorstrip Remove vectors from the ends of nucleotide sequence(s)
yank Add a sequence reference (a full USA) to a list file

Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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