
                                 trimspace 



Function

   Remove extra whitespace from an ASCII text file

Description

   Replaces all white space with a single space. nospace removes all
   whitespace from the input sequence.

Usage

   Here is a sample session with trimspace


% trimspace 
Remove extra whitespace from an ASCII text file
ASCII text file: seqspace2.txt
ASCII text output file [seqspace2.trimspace]: 

   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    [*.trimspace] ASCII text output file

   Additional (Optional) qualifiers: (none)
   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. 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

                 Standard (Mandatory) qualifiers    Allowed values Default
   [-infile]
   (Parameter 1) ASCII text file        Input file  Required
   [-outfile]
   (Parameter 2) ASCII text output file Output file <*>.trimspace
                 Additional (Optional) qualifiers   Allowed values Default
                 (none)
                 Advanced (Unprompted) qualifiers   Allowed values Default
                 (none)

Input file format

   trimspace reads any text file.

  Input files for usage example

  File: seqspace2.txt

>X13776   Pseudomonas aeruginosa    amiC and amiR gene
 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

   trimspace rewrites the input file.

  Output files for usage example

  File: seqspace2.trimspace

>X13776 Pseudomonas aeruginosa amiC and amiR gene
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

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 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
   noreturn Remove carriage return from ASCII files
   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)
   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)

   Jon Ison (jison © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

   None
