READSEQ INFORMATION

What is READSEQ?

READSEQ is a tool for: (i) converting sequence data files from one format to some other format (eg GenBank to EMBL etc) (ii) The tool is also used to read a number of sequence data files into one file (ie it combines numerous data files into one).

Why convert data file formats or put multiple data files into one file?

Various authors have written bioinformatics software and authors have tended to use different data formats as input files for their programmes. It is easier to convert data format from one to another with READSEQ rather than edit the files using a word processor or with a text editor.

Are other file format conversion tools available?

Yes, there are several. However, I find that READSEQ is the most versatile of all these. Another tool that is useful for such conversions is called convert_aln (convert alignment formats).

Can READSEQ be run on other platforms?

Yes, a variety of platforms can be used. Please refer to the author's readme document below for this.

How do I run READSEQ from trishul?

All account holders on trishul can use the programme by typing READSEQ at the trishul prompt. Help is also available by typing READSEQ -h.

What data formats can be used as in put or output file?

A variety of formats with a variety of functions are available with the utility. These are outline below.

 * 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, 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.