Readseq version 2 (biosequence conversion) available for testing

Don Gilbert gilbertd at bio.indiana.edu
Tue Aug 10 12:41:18 EST 1999


  Readseq version 2.0j (august 1999)

  A program to read & reformat biosequences, and a package
  of methods for programmmers to incorporate into their software
  for this end.  This is version is written in the Java language.
  
  This release is available for testing.  Some debugging is still
  needed.  Your comments are welcome.  Find it at
  http://iubio.bio.indiana.edu/soft/molbio/readseq/java/, or
  ftp://iubio.bio.indiana.edu/molbio/readseq/java/
  
Programs available in the readseq.jar package 
--------------------
For the current help document, use a Java Runtime command of
  jre -cp readseq.jar help 

Graphic interface to Readseq (using Java swing)
  Usage: jre -cp readseq.jar iubio.readseq.app
  Macintosh users: See also Readseq.macapp, a small Mac Java application
  to launch readseq.jar without a jre commandline.

HTTP server common gateway interface to Readseq
  Web servers can run this program to provide biosequence conversion
  See for example http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi
  See the help document for usage information

Command line version (classic-readseq options are supported)
  Usage: jre -cp readseq.jar run [options] input-file(s)

  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)
    -t[ranslate=]io     translate input symbol [i] to output symbol [o]
                        use several -tio to translate several symbols
    -v[erbose]          Verbose progress
    -f[ormat=]#         Format number for output,  or
    -f[ormat=]Name      Format name for output
          see Formats   list below for names and numbers
    -inform[at]=#       input format number,  or
    -inform[at]=Name    input format name.  Assume input data is this format
    -ch[ecksum]         calculate & print checksum of sequences

   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

This program requires a Java runtime (jre) program, version 1.1.x 
These options and call format are compatible with the classic readseq (v.1992)
with exception of no -reverse option.

  Known biosequence formats:
 ID  Name             Read  Write  Int'leaf  Document 
  1  IG|Stanford      yes    yes        --        --   
  2  GenBank|GB       yes    yes        --       yes   
  3  NBRF             yes    yes        --        --  
  4  EMBL             yes    yes        --       yes  
  5  GCG              yes    yes        --        --  
  6  DNAStrider       yes    yes        --        -- 
  7  Fitch             --     --        --        --  
  8  Pearson|Fasta    yes    yes        --        --   
  9  Zuker             --     --        --        --  
 10  Olsen             --     --       yes        --  
 11  Phylip3.2        yes    yes       yes        --  
 12  Phylip|Phylip4   yes    yes       yes        --  
 13  Plain|Raw        yes    yes        --        --  
 14  PIR|CODATA       yes    yes        --        --  
 15  MSF              yes    yes       yes        -- 
 16  ASN.1             --     --        --        --  
 17  PAUP|NEXUS       yes    yes       yes        --  
 18  Pretty            --    yes       yes        --  
 19  BLAST            yes     --       yes        --  
 20  XML              yes    yes        --       yes   
   (Int'leaf = interleaved format; Document = documentation is parsed)

--------------------
--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu




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