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nospace
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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
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