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
Input file: abc.dat
Output file [abc.noreturn]: 

Command line arguments

   Mandatory qualifiers:
  [-infile]            infile     (no help text) infile value
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-infile]
(Parameter 1)
(no help text) infile value Input file Required
[-outfile]
(Parameter 2)
Output file name Output file <sequence>.noreturn
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

The input file is a text data file with unwanted trailing carriage returns.

Output file format

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 nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping the first few
splitterSplit a sequence into (overlapping) smaller sequences
swissparseRetrieves sequences from swissprot using keyword search
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.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.

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