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:6.4.0.0 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 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 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 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 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 Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of 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 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 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 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