[EMBOSS] remap and GCG mapplot

Stefanie Lager stefanielager at fastmail.ca
Thu Dec 4 10:25:14 UTC 2003 

The "Changelog" of TACG 4.0 says that it has been built on Solaris 5.8
(gcc) and on Mac OSX 10.2 .

Stefanie

"Change Log for tacg development

$Id: ChangeLog,v 1.1.1.1 2001/11/14 18:36:33 mangalam Exp $ 

2003.05.30 Harry Mangalam, hjm at tacgi.com 
 * fixed the ghostscript bug - still some problems in the generation
of the 
   postscript - not enuf error checking, but the thang executes as
it's supposed 
   toat least if the postscript is good.

2003.05.29 Harry Mangalam, hjm at tacgi.com 
 * minor fix to seqio.c to allow OSX to include <dirent.h>
 * removed fmax() declaration - there was no parallel function anyway - 
   looked like the floating point match to imax() but no code for it.
 * Fixed a bunch of stuff in the configure /make process so things don't 
   break on different platforms
 * updated the config.guess & config.sub to allow finding OSX
 * re-included getopt1.c so that it compiles on Solaris - otherwise 
   getopt_long doesn't get defined.
 * added the psprolog file to the tarball so --ps, --pdf can work.
 * added automatic making of newdist and tarball to automagically
build a distro -
   this now works very well and keeps track of the key files to include.
 * tested build procedure on sf compile farm on the following machines:
 
   - Debian 2.2 Intel SMP (gcc 2.95)
     Linux usf-cf-x86-linux-1 2.4.19 #1 SMP  i686 unknown
   
   - RedHat 7.3 Intel SMP (gcc 2.96)
     Linux usf-cf-x86-linux-2.cf.sourceforge.net 2.4.18-5smp #1 SMP \
     i686 unknown
   
   - Debian 3.0  Alpha (gcc 2.95.4)
     Linux usf-cf-alpha-linux-1 2.2.20 #2 alpha unknown
     
   - Debian SPARC (gcc 2.95)
     Linux usf-cf-sparc-linux-1 2.4.18 #2  sparc64 unknown
     
   - Solaris 5.8 (gcc )
      
   - Mac OSX 10.2 (gcc 3.1)
     Darwin ucf-cf-ppc-macosx-2 6.5 Darwin Kernel Version 6.5:  \
     root:xnu/xnu-344.32.obj~1/RELEASE_PPC  Power Macintosh powerpc
   

2003.05.19 Harry Mangalam, hjm at tacgi.com 
 * changed --idonly to have default as 1 (don't have to specify the
flag value)
 

2003.05.16 Harry Mangalam, hjm at tacgi.com 
 * tested vs the old readseq test sequences - seems to read all but
   test.m-paup and test.strider (ascii format).  Have to verify a 
   bit more and see what' not working.  Since I have the binary 
   strider format reader working - it might be useful to mod seqio 
   to do that as well using pcre.
 * fixed a BUG that filtered teh wrong enzyme (filtered on proto 
   index instead of proto[index])
 * added and cleaned up verbosity levels so that verbosity is 
   upwardly inclusive (ie -V3 contains all the verbosity of V1 and V2)
 * make install, make newdist, make tarball, make install_web added to
   Makefile.in and they seem to work altho install_web just tells the 
   user what to do - edit & run the web installer script.

2003.05.09 Harry Mangalam, hjm at tacgi.com 
 * removed all traces of udping.c and udp reporting from code.
 
2003.03.14 Harry Mangalam, hjm at tacgi.com  
 * RE contains .E_olap which is the size of the overlap,
   if any.  Could  be combined with -o to provide selection of REs
   that provide only 5' overhangs  of size 3, for example. currently
   -o5, -o0 -o3; could graft on a hack to allow  user to extend to
   add a number if 5 or 3 ie -o5,5 which would select only REs  that
   have a 5' overhang of length 5 - OK!  Done!


2003.02.25.23 Harry Mangalam, hjm at tacgi.com 
 * 2.25.03 - Brian Frist sez following work on both Linux and SOlaris:
   Fasta EMBL Genbank IG Plain NBRF Phylip3.2 Phylip MSF but there are
some 
   others that fail mysteriously on some platforms - not completely
solved yet..
 * Following worked on Linux but not on SOlaris:
   Phylip3.2 Phylip MSF

 * Following worked on Solaris but not on Linux:
   CODATA

 * and NONE of the other formats generated by readseq worked on either, 
   not even GCG
   This disagrees with running the test sequences from readseq thru it
tho..
   requires more investigation...

   
2002-11.23 Harry Mangalam, hjm at tacgi.com 
  * added code to add a '-' to site numbers when nonpals are found on the
    bottom strand (suggested by Stefanie Lager), so that Site output now
    includes both positive and negative numbers (all numbered relative
to the
    top strand tho).  Still need to add a mod to -S flag to optionally
enable 
    this, tho.
  * added and modified code to allow pattern labels longer than 10
chars - 
    now have to be #defined for building in tacg.h (MAX_PAT_NAME_LEN) and 
    then the RE struct is checked for the longest name and that length is 
    used for output, etc (stored in F.MaxPatNameLen).

2001-10-17 Harry Mangalam, hjm at tacgi.com 
   * Fixed BAD realloc bug in ReadEnz in which test for end of
alloc'ed mem in
      RE was  calculated wrong - basic math error.  Showed up bc
trying to do a
      bunch of matching with errors and the cal overflowed the end of RE.

2001-06-09 Harry Mangalam, hjm at tacgi.com  
  * Added & deleted a bunch of files from CVS to bring things up to date
  * made the Logging of Degens optional to save memory
  * brought tacg.1 man page more up to date.
  * "

> I had no success on Solaris and FreeBSD.
> So on what system should the version 3.5 compile ?
> Do you have any information from the author why the current
> version 4 is not available from sourceforge ?
> 
> Cheers,
> David.
> 
> 
> I don't know anything about MacOSX, but when I had problems with
> TACG on Linux Harry Mangalam sent me the latest TACG version 4.0,
> which solved my compilation problems.
> 
> Stefanie
> 
>> It looks good, but I tried to compiled it with MacOSX 10.3 and I
>> got a lot of errors...
>> 
>> Le 3 déc. 03, à 14:08, Stefanie Lager a écrit :
>> 
>>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>>> for some of the GCG applications missing in EMBOSS. Like
>>> 
>>> mapplot (tacg -l -s )
>>> map (tacg -T3,1 -sL )
>>> mapsort (tacg -cF2 )
>>> mapgel (tacg -g10 -s )
>>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>>> 
>>> Stefanie
>>> 
>>>> Hello,
>>>> 
>>>> I am writing for a request for emboss. It would be great that
>>>> emboss could integrate something similar to the very useful (my
>>>> point of view) GCG's program MAPPLOT (a graphical
>>>> representation of a restriction map). I am sure that could be
>>>> easily added to emboss's remap or restrict.
>>>> With this feature added I would definitively not use anymore
>>>> GCG. Any idea. Thanks for the great job.
>>>> Jean-Christophe
>>>> 
>>>> ________________________
>>>> Jean-Christophe Amé, PhD
>>>> U.P.R. 9003 du CNRS - Cancérogénèse et Mutagénèse Moléculaire
>>>> et Structurale
>>>> École Supérieure de Biotechnologie de Strasbourg
>>>> Pôle API
>>>> Parc d'innovation, Boulevard Sébastien Brant
>>>> BP 10413
>>>> 67412 ILLKIRCH CEDEX
>>>> France
>>>> 
>>>> tel.: 33 3 90 24 47 05
>>>> Fax.: 33 3 90 24 46 86
>>> 
>>> ________________________________________________________________
>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> ________________________
>> Jean-Christophe Amé, PhD
>> U.P.R. 9003 du CNRS - Cancérogénèse et Mutagénèse Moléculaire et
>> Structurale
>> École Supérieure de Biotechnologie de Strasbourg
>> Pôle API
>> Parc d'innovation, Boulevard Sébastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>> 
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
> 
> _________________________________________________________________
> http://fastmail.ca/ - Fast Secure Web Email for Canadians
> 
> 

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