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