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# Readme

- DISCLAIMER
- DOCUMENTATION

## 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  -- 1 Feb 93
    |  *
    |  * 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 has been updated. There have been a number of enhancements and a few bug corrections since the previous general release in Nov 91 (see below). If you are using earlier versions, I recommend you update to this release.

### Readseq is particularly useful as it automatically detects many sequence formats, and interconverts among them. Formats added to this release include

- 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.

### As well, Phylip format can now be used as input. Options to reverse-compliment and to degap sequences have been added. A menu addition for users of the GDE sequence editor is included.

### 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)
      Readseq.help (longer than 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

    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

### Recent 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
  1Feb93
- reverted Genbank output format to fixed left margin (change in 30 Dec release), so GDE and others relying on fixed margin can read this.