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newseq
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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:6.6.0.0
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
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 (c) 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
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