noreturn.txt

emboss的linux版本的源代码

                                 noreturn 



Function

   Removes carriage return from ASCII files

Description

   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
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 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 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

   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
   extractalign Extract regions from a sequence alignment
   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
   makenucseq   Creates random nucleotide sequences
   makeprotseq  Creates random protein 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