                                   nospace



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Function

   Remove whitespace from an ASCII text file

Description

   Removes all whitespace from the input sequence. trimspace replaces all
   white space with a single space.

Usage

   Here is a sample session with nospace


% nospace
Remove whitespace from an ASCII text file
ASCII text file: seqspace.txt
ASCII text output file [seqspace.nospace]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Remove whitespace from an ASCII text file
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     ASCII text file
  [-outfile]           outfile    [*.nospace] ASCII text output file

   Additional (Optional) qualifiers:
   -menu               menu       [all] Remove whitespace (Values: all (all
                                  whitespace); end (trailing whitespace);
                                  excess (multiple whitespace characters))

   Advanced (Unprompted) qualifiers: (none)
   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

   nospace reads any text file.

  Input files for usage example

  File: seqspace.txt

>X13776
 ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga
 actgcacgat ctacctggcg agcctggagc acgagcgggt tcgcttcgta
 cggcgctgag cgacagtcac aggagaggaa acggatggga tcgcaccagg
 agcggccgct gatcggcctg ctgttctccg aaaccggcgt caccgccgat
 atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg agcaactgaa
 ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc
 ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc
 aaccgggggg tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa
 ggcggtgatg ccggtggtcg agcgcgccga cgcgctgctc tgctacccga
 ccccctacga gggcttcgag tattcgccga acatcgtcta cggcggtccg
 gcgccgaacc agaacagtgc gccgctggcg gcgtacctga ttcgccacta
 cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa
 gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc
 gaggaaatct acattccgct gtatccctcc gacgacgact tgcagcgcgc
 cgtcgagcgc atctaccagg cgcgcgccga cgtggtcttc tccaccgtgg
 tgggcaccgg caccgccgag ctgtatcgcg ccatcgcccg tcgctacggc
 gacggcaggc ggccgccgat cgccagcctg accaccagcg aggcggaggt
 ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt
 acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc
 catggtttct tcccggagaa cgcgaccatc accgcctggg ccgaggcggc
 ctactggcag accttgttgc tcggccgcgc cgcgcaggcc gcaggcaact
 ggcgggtgga agacgtgcag cggcacctgt acgacatcga catcgacgcg
 ccacaggggc cggtccgggt ggagcgccag aacaaccaca gccgcctgtc
 ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc
 agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc
 gacgactggt ccgccagcat gggcggggga ccgctcccat gagcgccaac
 tcgctgctcg gcagcctgcg cgagttgcag gtgctggtcc tcaacccgcc
 gggggaggtc agcgacgccc tggtcttgca gctgatccgc atcggttgtt
 cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt gccggtggac
 gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc
 gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt
 acgaaagccc cgcggtgctc tcgcagatca tcgagctgga gtgccacggc
 gtgatcaccc agccgctcga tgcccaccgg gtgctgcctg tgctggtatc
 ggcgcggcgc atcagcgagg aaatggcgaa gctgaagcag aagaccgagc
 agctccagga ccgcatcgcc ggccaggccc ggatcaacca ggccaaggtg
 ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct
 gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg
 agttgctggg aaacgagccg tccgcctgag cgatccgggc cgaccagaac
 aataacaaga ggggtatcgt catcatgctg ggactggttc tgctgtacgt
 tggcgcggtg ctgtttctca atgccgtctg gttgctgggc aagatcagcg
 gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct gagcgcctgc
 gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa
 ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg
 ccaaccagtt cctcgag


Output file format

   nospace rewrites the input file.

  Output files for usage example

  File: seqspace.nospace

>X13776
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacggga
actgcacgatctacctggcgagcctggagcacgagcgggttcgcttcgta
cggcgctgagcgacagtcacaggagaggaaacggatgggatcgcaccagg
agcggccgctgatcggcctgctgttctccgaaaccggcgtcaccgccgat
atcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagcaactgaa
ccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc
ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgc
aaccggggggtacggttcctcgtgggctgctacatgtcgcacacgcgcaa
ggcggtgatgccggtggtcgagcgcgccgacgcgctgctctgctacccga
ccccctacgagggcttcgagtattcgccgaacatcgtctacggcggtccg
gcgccgaaccagaacagtgcgccgctggcggcgtacctgattcgccacta
cggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa
gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctc
gaggaaatctacattccgctgtatccctccgacgacgacttgcagcgcgc
cgtcgagcgcatctaccaggcgcgcgccgacgtggtcttctccaccgtgg
tgggcaccggcaccgccgagctgtatcgcgccatcgcccgtcgctacggc
gacggcaggcggccgccgatcgccagcctgaccaccagcgaggcggaggt
ggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgcctt
acttctccagcatcgatacgcccgccagccgggccttcgtccaggcctgc
catggtttcttcccggagaacgcgaccatcaccgcctgggccgaggcggc
ctactggcagaccttgttgctcggccgcgccgcgcaggccgcaggcaact
ggcgggtggaagacgtgcagcggcacctgtacgacatcgacatcgacgcg
ccacaggggccggtccgggtggagcgccagaacaaccacagccgcctgtc
ttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggc
agtcgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctc
gacgactggtccgccagcatgggcgggggaccgctcccatgagcgccaac
tcgctgctcggcagcctgcgcgagttgcaggtgctggtcctcaacccgcc
gggggaggtcagcgacgccctggtcttgcagctgatccgcatcggttgtt
cggtgcgccagtgctggccgccgccggaagccttcgacgtgccggtggac
gtggtcttcaccagcattttccagaatggccaccacgacgagatcgctgc
gctgctcgccgccgggactccgcgcactaccctggtggcgctggtggagt
acgaaagccccgcggtgctctcgcagatcatcgagctggagtgccacggc
gtgatcacccagccgctcgatgcccaccgggtgctgcctgtgctggtatc
ggcgcggcgcatcagcgaggaaatggcgaagctgaagcagaagaccgagc
agctccaggaccgcatcgccggccaggcccggatcaaccaggccaaggtg
ttgctgatgcagcgccatggctgggacgagcgcgaggcgcaccagcacct
gtcgcgggaagcgatgaagcggcgcgagccgatcctgaagatcgctcagg
agttgctgggaaacgagccgtccgcctgagcgatccgggccgaccagaac
aataacaagaggggtatcgtcatcatgctgggactggttctgctgtacgt
tggcgcggtgctgtttctcaatgccgtctggttgctgggcaagatcagcg
gtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagcgcctgc
gtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa
ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccg
ccaaccagttcctcgag


Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 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
   noreturn         Remove carriage return from ASCII files
   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)

   Jon Ison
   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

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
