
                                 noreturn 



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

   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. 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

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 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
   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
   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 all 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
   pasteseq Insert one sequence into another
   revseq Reverse and complement a nucleotide sequence
   seqret Reads and writes (returns) 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
   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)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

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
