EMBOSS: noreturn

| noreturn

## Wiki

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## Function

Remove carriage return from ASCII files

## Description

noreturn reads an input file of plain text containing unwanted carriage returns on the end of lines, and writes an output file which is identical to the input file, except that any trailing carriage returns are removed.

## Usage

Here is a sample session with noreturn

    % noreturn abc.dat
    Remove carriage return from ASCII files
    ASCII text output file [abc.noreturn]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Remove carriage return from ASCII files
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-infile]            infile     ASCII text file
      [-outfile]           outfile    [*.noreturn] ASCII text output file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -system             menu       [unix] Target operating system for
                                      end-of-line format (Values: unix (Unix/Linux
                                      systems); pc (Windows/DOS); mac (Apple
                                      Macintosh))

       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory2        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
[-infile] (Parameter 1) | infile | ASCII text file | Input file | Required
[-outfile] (Parameter 2) | outfile | ASCII text output file | Output file | <*>.noreturn
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-system | list | Target operating system for end-of-line format |
unix | (Unix/Linux systems)
pc | (Windows/DOS)
mac | (Apple Macintosh)
| unix
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | 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

The input file is a text data file with unwanted trailing carriage returns.

### Input files for usage example

### File: abc.dat

    >ABC Test sequence with PC carriage return format
    ACDEFGHIKLMNPQRSTVWY

## Output file format

### Output files for usage example

### File: abc.noreturn

    >ABC Test sequence with PC carriage return format
    ACDEFGHIKLMNPQRSTVWY

The output file is identical to the input file, except that any trailing carriage returns have been removed. For most files this will make no difference.

## Data files

None.

## Notes

Unix and PC operating systems store plain text files (which includes sequence files) slightly differently. Unix files have a hidden character called 'new line' at the end of every line whereas PC files have a 'new line' and a 'carriage return' at the end of every line. When files are transferred from a PC to a Unix machines, it is often useful to convert the file from the PC format to the Unix format, otherwise commands (such as 'more') and programs (such as text editors) that display the file can become confused. noreturn removes 'carriage return' characters from such files, converting them from PC format to Unix format text files.

EMBOSS programs can read in both PC and Unix text file formats, so it is not necessary for you to use this utility all of the time.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 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
newseq | Create a sequence file from a typed-in sequence
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file
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)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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

## History

Written (1999) - Alan Bleasby

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None