diff GEMBASSY-1.0.3/src/ggeneskew.c @ 2:8947fca5f715 draft default tip

Uploaded

--- a/GEMBASSY-1.0.3/src/ggeneskew.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,208 +0,0 @@
-/******************************************************************************
-** @source ggeneskew
-**
-** Calculate the gene strand bias of the given genome
-**
-** @author Copyright (C) 2012 Hidetoshi Itaya
-** @version 1.0.3
-** @modified 2012/1/20  Hidetoshi Itaya  Created!
-** @modified 2013/6/16  Revision 1
-** @modified 2015/2/7   Refactor
-** @@
-**
-** This program is free software; you can redistribute it and/or
-** modify it under the terms of the GNU General Public License
-** as published by the Free Software Foundation; either version 2
-** of the License, or (at your option) any later version.
-**
-** This program is distributed in the hope that it will be useful,
-** but WITHOUT ANY WARRANTY; without even the implied warranty of
-** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-** GNU General Public License for more details.
-**
-** You should have received a copy of the GNU General Public License
-** along with this program; if not, write to the Free Software
-** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
-******************************************************************************/
-
-#include "emboss.h"
-#include "glibs.h"
-
-
-
-
-/* @prog ggeneskew ************************************************************
-**
-** Calculate the gene strand bias of the given genome
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggeneskew", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq = NULL;
-
-  ajint	 window     = 0;
-  ajint	 slide      = 0;
-  AjBool cumulative = ajFalse;
-  AjBool gc3        = ajFalse;
-  AjPStr basetype   = NULL;
-
-  AjBool accid  = ajFalse;
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  AjPFile tmpfile = NULL;
-  AjPStr  tmpname = NULL;
-
-  AjBool      plot = 0;
-  AjPFile     outf = NULL;
-  AjPFilebuff buff = NULL;
-  AjPGraph    mult = NULL;
-
-  gPlotParams gpp;
-  AjPStr      title = NULL;
-
-  seqall     = ajAcdGetSeqall("sequence");
-  window     = ajAcdGetInt("window");
-  slide      = ajAcdGetInt("slide");
-  cumulative = ajAcdGetBoolean("cumulative");
-  gc3        = ajAcdGetBoolean("gctri");
-  basetype   = ajAcdGetSelectSingle("base");
-  accid      = ajAcdGetBoolean("accid");
-
-  plot = ajAcdGetToggle("plot");
-  outf = ajAcdGetOutfile("outfile");
-  mult = ajAcdGetGraphxy("graph");
-
-  if(ajStrMatchC(base, "none"))
-    basetype = ajStrNewC("");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      inseq = NULL;
-
-      if(!accid)
-        {
-          if(gFormatGenbank(seq, &inseq))
-            {
-              gAssignUniqueName(&tmpname);
-
-              tmpfile = ajFileNewOutNameS(tmpname);
-
-              if(!tmpfile)
-                {
-                  ajFmtError("Output file (%S) open error\n", tmpname);
-                  embExitBad();
-                }
-
-              ajFmtPrintF(tmpfile, "%S", inseq);
-              ajFileClose(&tmpfile);
-              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-              gFilePostSS(url, tmpname, &restid);
-              ajStrDel(&url);
-              ajSysFileUnlinkS(tmpname);
-            }
-          else
-            {
-              ajFmtError("Sequence does not have features\n"
-                         "Proceeding with sequence accession ID\n");
-              accid = ajTrue;
-            }
-        }
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      if(accid)
-        {
-          ajStrAssignS(&restid, seqid);
-          if(ajStrGetLen(seqid) == 0)
-            {
-              ajDie("Cannot proceed without header with -accid\n");
-            }
-
-          if(!gValID(seqid))
-            {
-              ajDie("Invalid accession ID:%S, exiting\n", seqid);
-            }
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/geneskew/window=%d/slide=%d/"
-                  "cumulative=%d/gc3=%d/base=%S/output=f/tag=gene",
-                  base, restid, window, slide, cumulative, gc3, basetype);
-
-      if(plot)
-        {
-          title = ajStrNew();
-
-          ajStrAppendC(&title, argv[0]);
-          ajStrAppendC(&title, " of ");
-          ajStrAppendS(&title, seqid);
-
-          gpp.title = ajStrNewS(title);
-          gpp.xlab = ajStrNewC("gene skew");
-          gpp.ylab = ajStrNewC("bp");
-
-          if(!gFilebuffURLS(url, &buff))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-
-          if(!gPlotFilebuff(buff, mult, &gpp))
-            {
-              ajDie("Error in plotting\n");
-            }
-
-          AJFREE(gpp.title);
-          AJFREE(gpp.xlab);
-          AJFREE(gpp.ylab);
-          ajStrDel(&title);
-          ajFilebuffDel(&buff);
-        }
-      else
-        {
-          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
-          if(!gFileOutURLS(url, &outf))
-            {
-              ajDie("File downloading error from:\n%S\n", url);
-            }
-        }
-
-      ajStrDel(&url);
-      ajStrDel(&restid);
-      ajStrDel(&seqid);
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&base);
-
-  embExit();
-
-  return 0;
-}