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:6.4.0.0 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 [.] 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 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 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