EMBOSS: newseq manual

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:6.6.0.0

   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

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)

[-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

-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

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

-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

-warning

boolean

Report warnings

Boolean value Yes/No

-error

boolean

Report errors

Boolean value Yes/No

-fatal

boolean

Report fatal errors

Boolean value Yes/No

-die

boolean

Report dying program messages

Boolean value Yes/No

-version

boolean

Report version number and exit

Boolean value Yes/No

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.

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

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

Wiki

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