[EMBOSS] Kaptain user interface, new release

[Thomas Siegmund]

*This message was transferred with a trial version of CommuniGate(tm) Pro*
Hi everybody,

there is a new release of the EMBOSS.kaptn graphical user interface for EMBOSS 
running on Linux/X11 or MacOSX. Version 0.96 of the GUI is basically a bugfix 
release for use with EMBOSS 2.8.0.

Due to considerable efforts of the EMBOSS programmers towards a more 
consistent command line interface many emboss qualifiers have been changed or 
renamed during the last few EMBOSS releases. Unfortunately many of these 
changes were not listed in the EMBOSS ChangeLog. Therefore EMBOSS and the GUI 
have drifted apart to an unacceptable degree.

In order to fix this I made a little script to check the kaptain grammars 
against the acd files of a given EMBOSS release. I now have fixed all the 
problems shown by the script running against EMBOSS 2.8.0 . I'd recommend 
everybody using the Kaptain GUI with EMBOSS 2.8.0 to get the 0.96 version of 
the GUI. As you can see from the ChangeLog there were quite a few fixes to 
do :-0

Download, as usual, from 

http://userpage.fu-berlin.de/~sgmd/download.html

From the ChangeLog:

Version 0.96 - Use with EMBOSS 2.8
----------------------------------------------
- -startbase, -endbase, -separate for abiview.kaptn
- -aadata  for charge.kaptn
- -addlast , -report -> -outfile for checktrans.kaptn
- -sum for chips.kaptn
- -seqout -> -outseq in coderet.kaptn
- -obsexp, -cg, -pc and a new layout for cpgplot.kaptain
- small fix for cutgextract
- -aadata for digest.kaptn
- -maxrepeat for einverted
- -full for embossversion
- -nhydrophylic -> nohgap in emma.kaptn
- -onlydend for emma.kaptn
- -sequences -> -sequence in emowse.kaptn
- -aadata for emowse.kaptn
- removed -mmshow- -raccshow, and  -rdescshow from fuzznuc.kaptn,
  fuzzpro.kaptn, fuzztran.kaptn
- maxsize for getorf.kaptn
- -gi, -version for infoseq.kaptn
- -interticks for lindna.kapnt
- -outlist -> -outfile in listor.kaptn
- -report -> outfile in megamerger.kaptn
- -other -> -othersequence in merger.kaptn
- -showdel for mwfilter.kaptn
- -brief for needle.kaptn
- -sequencea -> -sequence in octanol.kaptn
- -insequence -> -sequence in palindrome.kaptn
- -sequence,-insseq -> -[ab]sequence
   and a cleaner layout for pasteseq.kaptn
- -insseq -> -sequence for pepinfo.kaptn
- -aadata for pepstats.kaptn
- -wheel for pepwheel.kaptn
- -msf -> -sequences for pepwindowall.kaptn
- -msf -> -sequences, remove -nodata in plotcon.kaptn
- -start, -stop for plotorf.kaptn
- -msf -> -sequences for prettyplot.kaptn
- -sequence -> -seqall for primersearch.kaptn
- added -name, -description, removed -preferred from remap.kaptn
- added -blunt, -sticky, removed -preferred from remap.kaptn
- added -datafile, removed -preferred from restrict.kaptn
- -feature for seqret.kaptn
- -strittags for showfeat.kaptn
- remove -preferred from showseq.kaptn
- -primers -> -primersfile, -sequences -> -seqall in stssearch.kaptn
- -msf -> -sequences in tmap.kaptn
- -nseq -> -asequence, -pseq -> -bsequence in tranalign.kaptn
- -feature for skipseq.kaptn
- -gapextend, -gapopen for supermatcher.kaptn
- -casesensitive for textsearch.kaptn (doesn't seem to work)
- -minlength, -custom for tfscan.kaptn
- -brief for water.kaptn
- added kaptncheck.pl, a quick hack to compare kaptain grammars
  with the acd files of a given EMBOSS release
- added sixpack.kaptn

Version 0.95 "Bangkok edition"
- remove -data in pepwheel.kapnt, pepnet.kaptn
- make -msf -sequence in all ephylip programms
- small fixes in needle.kaptn, water.kaptn

Version 0.94
- renamed pestfind.kaptn to epestfind.kaptn
- sequencea -> sequence in pepstats.kaptn
- rformat option for dreg.kaptn, preg.kaptn, recoder.kaptn, silent.kaptn

Regards,

Thomas

-- 
Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

E-Mails können unvollständig oder fehlerhaft oder manipuliert sein. Sie
dienen daher stets nur der Information. Rechtsverbindliche
Willenserklärungen müssen in Schriftform, d.h. mindestens per Telefax mit
Unterschrift des Erklärenden, abgegeben werden, um wirksam zu sein. Unsere
E-Mails sind stets vertraulich und nur für den angegebenen Adressaten
bestimmt. Andere Empfänger werden gebeten, diese Nachricht zu löschen. Jede
unberechtigte Weiterleitung ist untersagt. Trotz ergriffener
Vorsichtsmaßnahmen gegen Viren kann keine Haftung für etwaige Schäden aus
der Verwendung dieser E-Mail übernommen werden.

E-mails may be incomplete or be subject to change without notice. Therefore
the content of this E-mail is not binding unless confirmed by letter or by
telefax with signature of the author. Our E-mails are confidential and
dedicated to the intended recipient only. If you are not an intended
recipient, please delete the original message and all copies. Any
unauthorized distribution is strictly prohibited. Although precautions have
been taken to prevent the existence of viruses in this E-mail, the company
cannot accept any responsibility for any damage arising out of or from the
use of this E-mail.