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    Readseq.help

    DISCLAIMER

    This file has been automatically converted from the original documentation for easy use inside the ARB help system. Differences compared with the original documentation are unintentionally caused by the conversion process. In doubt please refer to the original documentation!

     

    DOCUMENTATION

    |  * ReadSeq.Help -- 30 Dec 92
    |  *
    |  * Reads and writes nucleic/protein sequences in various
    |  * formats. Data files may have multiple sequences.
    |  *
    |  * Copyright 1990 by d.g.gilbert
    |  * biology dept., indiana university, bloomington, in 47405
    |  * e-mail: gilbertd@bio.indiana.edu
    |  *
    |  * This program may be freely copied and used by anyone.
    |  * Developers are encourged to incorporate parts in their
    |  * programs, rather than devise their own private sequence
    |  * format.
    |  *
    |  * This should compile and run with any ANSI C compiler.
    |  * Please advise me of any bugs, additions or corrections.

    Readseq is particularly useful as it automatically detects many sequence formats, and interconverts among them.

    Formats which readseq currently understands:

    • IG/Stanford, used by Intelligenetics and others
    • GenBank/GB, genbank flatfile format
    • NBRF format
    • EMBL, EMBL flatfile format
    • GCG, single sequence format of GCG software
    • DNAStrider, for common Mac program
    • Fitch format, limited use
    • Pearson/Fasta, a common format used by Fasta programs and others
    • Zuker format, limited use. Input only.
    • Olsen, format printed by Olsen VMS sequence editor. Input only.
    • Phylip3.2, sequential format for Phylip programs
    • Phylip, interleaved format for Phylip programs (v3.3, v3.4)
    • Plain/Raw, sequence data only (no name, document, numbering)
    • MSF multi sequence format used by GCG software
    • PAUP's multiple sequence (NEXUS) format
    • PIR/CODATA format used by PIR
    • ASN.1 format used by NCBI
    • Pretty print with various options for nice looking output. Output only.

    See the included "Formats" file for detail on file formats.

    Example usage:
      readseq
          -- for interactive use
    readseq my.1st.seq  my.2nd.seq  -all  -format=genbank  -output=my.gb
        -- convert all of two input files to one genbank format output file
    readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match
        -- output to standard output a file in a pretty format
    readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev
        -- select 4 items from input, degap, reverse, and uppercase them
    cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
        -- pipe a bunch of data thru readseq, converting all to asn

    The brief usage of readseq is as follows. The "[]" denote optional parts of the syntax:

    readseq -help
    readSeq (27Dec92), multi-format molbio sequence reader.
    usage: readseq [-options] in.seq > out.seq
     options
        -a[ll]         select All sequences
        -c[aselower]   change to lower case
        -C[ASEUPPER]   change to UPPER CASE
        -degap[=-]     remove gap symbols
        -i[tem=2,3,4]  select Item number(s) from several
        -l[ist]        List sequences only
        -o[utput=]out.seq  redirect Output
        -p[ipe]        Pipe (command line, <stdin, >stdout)
        -r[everse]     change to Reverse-complement
        -v[erbose]     Verbose progress
        -f[ormat=]#    Format number for output,  or
        -f[ormat=]Name Format name for output:
           |  1. IG/Stanford           10. Olsen (in-only)
           |  2. GenBank/GB            11. Phylip3.2
           |  3. NBRF                  12. Phylip
           |  4. EMBL                  13. Plain/Raw
           |  5. GCG                   14. PIR/CODATA
           |  6. DNAStrider            15. MSF
           |  7. Fitch                 16. ASN.1
           |  8. Pearson/Fasta         17. PAUP
           |  9. Zuker                 18. Pretty (out-only)
    Pretty format options:
     -wid[th]=#            sequence line width
     -tab=#                left indent
     -col[space]=#         column space within sequence line on output
     -gap[count]           count gap chars in sequence numbers
     -nameleft, -nameright[=#]   name on left/right side [=max width]
     -nametop              name at top/bottom
     -numleft, -numright   seq index on left/right side
     -numtop, -numbot      index on top/bottom
     -match[=.]            use match base for 2..n species
     -inter[line=#]        blank line(s) between sequence blocks

    Notes:

    In use, readseq will respond to command line arguments, or to interactive use. Command line arguments cannot be combined but must each follow a switch character (-). In this release, the command line options are now words, with an equals (=) to separate parameter(s) fromt he command. You cannot put a space between a command and its parameter, as is usual for Unix programs (this is to preserve compatibility with VMS). The command line syntax of the earlier versions is still supported.

    See the file Formats for details of the sequence formats which are supported by readseq. The auto-detection feature of readseq which distinguishes these formats looks for some of the unique keywords and symbols that are found in each format. It is not infallible at this, though it attempts to exclude unknown formats. In general, if you feed to readseq a sequence file that you know is one of these common formats, you are okay. If you feed it data that might be oddball formats, or non-sequence data, you might well get garbage results. Also, different developers are always thinking up minor twists on these common formats (like PAUP requiring a blank line between blocks of Phylip format, or IG adding form feeds between sequences), which may cause hassles.

    In general, output supports only minimal subsets of each format needed for sequence data exchanges. Features, descriptions and other format-unique information is discarded.

    The pretty format requires additional options to generate a nice output. Try the various pretty options to see what you like. Pretty format is OUPUT only, readseq cannot read a Pretty format file.

    Readseq is NOT optimized for LARGE files. It generally makes several reads thru each input file (one per sequence output at present, future version may optimize this). It should handle input and output files and sequences of any size, but will slow down quite a bit for very large (multi megabyte) sized files. It is NOT recommended for converting databanks or large subsets there-of. It is primarily directed at the small files that researchers use to maintain their personal data, which they frequently need to interconvert for the various analysis programs which so frequently require a special format.

    Users of Olsen multi sequence editor (VMS). The Olsen format
    here is produced with the print command:
      print/out=some.file
    Use Genbank output from readseq to produce a format that this
    editor can read, and use the command
      load/genbank some.file
    Dan Davison has a VMS program that will convert to/from the
    Olsen native binary data format. E-mail davison@uh.edu

    Warning: Phylip format input is now supported (30Dec92), however the auto-detection of Phylip format is very probabilistic and messy, especially distinguishing sequential from interleaved versions. It is not recommended that one use readseq to convert files from Phylip format to others unless essential.

    This program is available thru Internet gopher, as

    gopher ftp.bio.indiana.edu browse into the IUBio-Software+Data/molbio/readseq/ folder select the readseq.shar document
    Or thru anonymous FTP in this manner:
      my_computer> ftp  ftp.bio.indiana.edu  (or IP address 129.79.224.25)
        username:  anonymous
        password:  my_username@my_computer
      ftp> cd molbio/readseq
      ftp> get readseq.shar
      ftp> bye

    readseq.shar is a Unix shell archive of the readseq files. This file can be editted by any text editor to reconstitute the original files, for those who do not have a Unix system or an Unshar program. Read the top of this .shar file for further instructions.

    There are also pre-compiled executables for the following computers: Silicon Graphics Iris, Sparc (Sun Sparcstation & clones), VMS-Vax, Macintosh. Use binary ftp to transfer these, except Macintosh. The Mac version is just the command-line program in a window, not very handy.

    C source files:
      readseq.c ureadseq.c ureadasn.c ureadseq.h
    Document files:
      Readme (this doc)
      Formats (description of sequence file formats)
      add.gdemenu (GDE program users can add this to the .GDEmenu file)
      Stdfiles -- test sequence files
      Makefile -- Unix make file
      Make.com -- VMS make file
      *.std    -- files for testing validity of readseq

    Recent changes (see also readseq.c for all history of changes):

    4 May 92

    • added 32 bit CRC checksum as alternative to GCG 6.5bit checksum
      Aug 92
    • fixed Olsen format input to handle files w/ more sequences, not to mess up when more than one seq has same identifier, and to convert number masks to symbols.
    • IG format fix to understand ^L
      30 Dec 92
    • revised command-line & interactive interface. Suggested form is now
      readseq infile -format=genbank -output=outfile -item=1,3,4 ...
      but remains compatible with prior commandlines:
      readseq infile -f2 -ooutfile -i3 ...
    • added GCG MSF multi sequence file format
    • added PIR/CODATA format
    • added NCBI ASN.1 sequence file format
    • added Pretty, multi sequence pretty output (only)
    • added PAUP multi seq format
    • added degap option
    • added Gary Williams (GWW, G.Williams@CRC.AC.UK) reverse-complement option.
    • added support for reading Phylip formats (interleave & sequential)
    • string fixes, dropped need for compiler flags NOSTR, FIXTOUPPER, NEEDSTRCASECMP
    • changed 32bit checksum to default, -DSMALLCHECKSUM for GCG version