|
noreturn |
Function
Removes carriage return from ASCII filesDescription
The way that Unix and PC operating systems store simple text files, (including sequence files), differs slightly.Unix files have a hidden character called 'new line' at the end of every line.
PC files have two hidden characters called 'carriage return' and then 'new line' at the end of every line.
When files are transferred from PC machines to Unix machines, it is often useful to convert the file from the PC format to the Unix format, otherwise commands like 'more', to display the file, and text editors can become confused.
This simple utility 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.
Usage
Here is a sample session with noreturn
% noreturn abc.dat Removes carriage return from ASCII files Output file [abc.noreturn]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-infile] infile Input file
[-outfile] outfile Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-system menu Target operating system for end-of-line
format
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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. 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 deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||
|---|---|---|---|---|---|---|---|---|---|
| [-infile] (Parameter 1) |
Input file | Input file | Required | ||||||
| [-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.noreturn | ||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||
| (none) | |||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
| -system | Target operating system for end-of-line format |
|
unix | ||||||
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
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 |
|---|---|
| biosed | Replace or delete sequence sections |
| codcopy | Reads and writes a codon usage table |
| cutseq | Removes a specified section from a sequence |
| degapseq | Removes gap characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Reads and writes (returns) flatfile entries |
| extractfeat | Extract features from a sequence |
| extractseq | Extract regions from a sequence |
| listor | Write a list file of the logical OR of two sets of sequences |
| maskfeat | Mask off features of a sequence |
| maskseq | Mask off regions of a sequence |
| newseq | Type in a short new sequence |
| notseq | Exclude a set of sequences and write out the remaining ones |
| nthseq | Writes one sequence from a multiple set of sequences |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads and writes (returns) sequences in individual files |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| splitter | Split a sequence into (overlapping) smaller sequences |
| trimest | Trim poly-A tails off EST sequences |
| trimseq | Trim ambiguous bits off the ends of sequences |
| union | Reads sequence fragments and builds one sequence |
| vectorstrip | Strips out DNA between a pair of vector sequences |
| yank | Reads a sequence range, appends the full USA to a list file |
Author(s)
Alan Bleasby (ajb © ebi.ac.uk)European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK