                                  noreturn



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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:6.6.0.0

   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


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 (c) 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
