pregap4 interactive editing error

  • Mac OSX 10.3.8, Staden 1.5.3

    I have just hit a strange error. In pregap4, if I load in a lot of trace files, and let them assemble automatically, everything goes fine. If I interactively edit any of the trace files I am asked if I want to save them before moving to the next file. If I do save them, those edited files get flagged as not being in .exp format when being assembled into a gap4 database. If I look at the failed .exp files, they are not in .exp text format but in .ztr format (looks like binary stuff in a text editor). Non-edited .exp files are in correct format. It looks like the pregap4 .exp save is acting strangely. Any comments would be welcome.

    • James Bonfield
      James Bonfield

      Please see for discussion and a cure.

      Put simply, it's a bug in the trev tcl code so is easy enough to fix by installing a new trev.tcl in the appropriate location.


      PS. Yes I know it's about time for a new release! I've got a number of existing bugs to work through before that though.

    • Thanks James, that has solved the problem nicely. I must say that I am getting to like the staden package very much. I have used sequencher in the past but have become increasingly frustrated with their pricing and lack of improvements over the last 5 years.
      regards, Mike D-S
      University of Melbourne

    • After replacing the trev.tcl file I get this error message. Is there something else I have to change?

      Tue 05 Apr 19:00:20 2005 interactive_clip::run: unknown option "-trace_scale"
          while executing
      "dnatrace $trace.t  -relief ridge -bd 3  -xscrollcommand "$trace.s set"  -shownumbers $tdisp(n)  -showsequence $tdisp(s)  -showedits $tdisp(e)  -showtr..."
          (procedure "CreateTraceWin" line 4)
          invoked from within
      "CreateTraceWin [keylget trev_defs TRACE.WIN] $xmag $ymag $trace_scale"
          (procedure "CreateTrevWin" line 36)
          invoked from within
      "CreateTrevWin $xmag $ymag $pregap_mode $block_scf $edit $trace_scale"
          (file "/Users/mikeds/Applications/staden-macosx-1-5-3/macosx-bin/../lib/trev/trev.tcl" line 1543)

    • James Bonfield
      James Bonfield

      Please use revision 1.2 of the trev.tcl file as the newer versions have diverged too much from the 1.5.3 code base. (Ie if you fetched code revision 1.4 then you'd also ened to update tk_utils C library, recompile, etc etc).

      Alternatively use the viewcvs "diff" to see what I changed to fix the bug:

      These fixes could be manually applied to the original trev.tcl too (assuming you still have it :-)).


    • Maybe I have a more serious problem. I went back to version 1.2 of Trev.tcl, and I have the same problem as with 1.3, the .exp files are written out wrongly when I save after editing in pregap4. Maybe I should compile from source. Are there instructions for doing this? (do I need specific flags for OS X?)
      Regards, Mike

    • James Bonfield
      James Bonfield

      Hmm, the 1.2 version of trev.tcl *should* fix the bug, so I'm not confused. Have you put it in the lib/trev/trev.tcl directory (rather than in src, which is just where the source tree has it)?

      As for compiling from source, it's doable, but non-trivial. Compiling from source for the 1.5.3 release obviously wouldn't cure the issue either. You'd need to check out the latest code from CVS which by all means do (it seems pretty stable and I try not to upload stuff until I've tested it at least works on my own system), but it hasn';t been compiled on MacOSX for a while.

      There's a which outlines the basics needed to get things going. The third-party libraries required (png, zlib, tcl, tk, itcl, iwidgets, etc maybe!) have a makefile which hopefully will be able to download, configure and appropriately build them for you.


    • I've tried several versions of trev.tcl, I tried modifying using diff (taking out the trace_scale stuff from v 1.4 or adding the non-trace_scale stuff to v 1.3). I am putting it in the right place, as I get errors specific to the version of trev.tcl
        At present I can live with not being able to interactively edit in the pregap4 assembly phase. Has anyone considered putting staden in fink? Also, has anyone thought about integrating staden with the phylogeny program ARB? It would be so nice to go from the ARB sequence editor to the actual aligned chromatograms to check sequences.

      • aamadio

        I have the same problem and I really need to interact to clip.
        I tried all the version of trev.tcl, and manual editing. In some of them an error message apperars, in others, the problem is not solved.
        Any help?

        I have the version 1.5.3 on WinXP

    • James Bonfield
      James Bonfield

      Sounds like it's definitely time to start packaging up a new distribution. This bug has been fixed, but if it's hard to get the right version such that newer incompatibilities don't add other problerms then it's best to solve by updating everything at once.

      I've been meaning to do this for ages, but it can be a lengthy process building all the various distributions.