noreturn 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 carriage return from ASCII files Description noreturn reads an input file of plain text containing unwanted carriage returns on the end of lines, and writes an output file which is identical to the input file, except that any trailing carriage returns are removed. Usage Here is a sample session with noreturn % noreturn abc.dat Remove carriage return from ASCII files ASCII text output file [abc.noreturn]: Go to the input files for this example Go to the output files for this example Command line arguments Remove carriage return from ASCII files Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] infile ASCII text file [-outfile] outfile [*.noreturn] ASCII text output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -system menu [unix] Target operating system for end-of-line format (Values: unix (Unix/Linux systems); pc (Windows/DOS); mac (Apple Macintosh)) 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 The input file is a text data file with unwanted trailing carriage returns. Input files for usage example File: abc.dat >ABC Test sequence with PC carriage return format ACDEFGHIKLMNPQRSTVWY Output file format Output files for usage example File: abc.noreturn >ABC Test sequence with PC carriage return format ACDEFGHIKLMNPQRSTVWY 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 Unix and PC operating systems store plain text files (which includes sequence files) slightly differently. Unix files have a hidden character called 'new line' at the end of every line whereas PC files have a 'new line' and a 'carriage return' at the end of every line. When files are transferred from a PC to a Unix machines, it is often useful to convert the file from the PC format to the Unix format, otherwise commands (such as 'more') and programs (such as text editors) that display the file can become confused. noreturn 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. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with a status of 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 nospace Remove 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 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) Alan Bleasby 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 Written (1999) - Alan Bleasby Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None