newseq |
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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.
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
Create a sequence file from a typed-in sequence Version: EMBOSS:6.4.0.0 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 [ |
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 | ||||
[-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 |
ID cytoc Unreviewed; 12 AA. DE fragment of cytochrome c SQ SEQUENCE 12 AA; 1464 MW; 6F142FA88DADC40B CRC64; KKKEERADLI AY // |
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.
Program name | Description |
---|---|
aligncopy | Reads and writes alignments |
aligncopypair | Reads and writes pairs from alignments |
biosed | Replace or delete sequence sections |
codcopy | Copy and reformat a codon usage table |
cutseq | Removes a section from a sequence |
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
descseq | Alter the name or description of a sequence |
entret | Retrieves 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 | Reads and writes a feature table |
featreport | Reads and writes 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 | Masks all ambiguity characters in nucleotide sequences with N |
maskambigprot | Masks 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 | Reads and writes (returns) one set of sequences from many |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a nucleotide sequence |
seqcount | Reads and counts sequences |
seqret | Reads and writes (returns) sequences |
seqretsetall | Reads and writes (returns) many sets of sequences |
seqretsplit | Reads sequences and writes them to individual files |
sizeseq | Sort sequences by size |
skipredundant | Remove redundant sequences from an input set |
skipseq | Reads and writes (returns) 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 | Removes vectors from the ends of nucleotide sequence(s) |
yank | Add a sequence reference (a full USA) to a list file |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.