Readme

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|  * 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

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