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noreturn |
Wiki
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Function
Remove carriage return from ASCII filesDescription
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:6.6.0.0
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 | ||||||
| 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 BleasbyEuropean 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.