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

Uploaded

--- a/GEMBASSY-1.0.3/src/ggcsi.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,192 +0,0 @@
-/******************************************************************************
-** @source ggcsi
-**
-** GC Skew Index: an index for strand-specific mutational bias
-**
-** @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   RESTify
-** @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 ggcsi ****************************************************************
-**
-** GC Skew Index: an index for strand-specific mutational bias
-**
-******************************************************************************/
-
-int main(int argc, char *argv[])
-{
-  embInitPV("ggcsi", argc, argv, "GEMBASSY", "1.0.3");
-
-  AjPSeqall seqall;
-  AjPSeq    seq;
-  AjPStr    inseq   = NULL;
-
-  AjPStr restid = NULL;
-  AjPStr seqid  = NULL;
-
-  AjPStr base = NULL;
-  AjPStr url  = NULL;
-
-  ajint	 window  = 0;
-  AjBool at      = 0;
-  AjBool purine  = 0;
-  AjBool keto    = 0;
-  AjBool pval    = 0;
-  AjPStr version = NULL;
-
-  AjPStr      tmpname = NULL;
-  AjPSeqout   tmpout  = NULL;
-  AjPFilebuff tmpbuff = NULL;
-
-  AjPStr tmp   = NULL;
-  AjPStr parse = NULL;
-  AjPStr gcsi  = NULL;
-  AjPStr sa    = NULL;
-  AjPStr dist  = NULL;
-  AjPStr z     = NULL;
-  AjPStr p     = NULL;
-
-  AjPStrTok handle  = NULL;
-
-  AjPFile outf = NULL;
-
-  seqall  = ajAcdGetSeqall("sequence");
-  window  = ajAcdGetInt("window");
-  at      = ajAcdGetBoolean("at");
-  purine  = ajAcdGetBoolean("purine");
-  keto    = ajAcdGetBoolean("keto");
-  pval    = ajAcdGetBoolean("pval");
-  version = ajAcdGetSelectSingle("gcsi");
-  outf    = ajAcdGetOutfile("outfile");
-
-  base = ajStrNewC("rest.g-language.org");
-
-  gAssignUniqueName(&tmpname);
-  ajStrAppendC(&tmpname, ".fasta");
-
-  while(ajSeqallNext(seqall, &seq))
-    {
-      tmpout = ajSeqoutNew();
-
-      if(!ajSeqoutOpenFilename(tmpout, tmpname))
-        {
-          embExitBad();
-        }
-
-      ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
-      ajSeqoutWriteSeq(tmpout, seq);
-      ajSeqoutClose(tmpout);
-      ajSeqoutDel(&tmpout);
-
-      ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
-      gFilePostSS(url, tmpname, &restid);
-      ajStrDel(&url);
-      ajSysFileUnlinkS(tmpname);
-
-      ajStrAssignS(&seqid, ajSeqGetAccS(seq));
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajStrAssignS(&seqid, ajSeqGetNameS(seq));
-        }
-
-      if(ajStrGetLen(seqid) == 0)
-        {
-          ajWarn("No valid header information\n");
-        }
-
-      url = ajStrNew();
-
-      ajFmtPrintS(&url, "http://%S/%S/gcsi/window=%d/at=%d/purine=%d/"
-                  "keto=%d/p=%d/version=%d/", base, restid, window, at, purine,
-                  keto, pval, version);
-
-      if(!gFilebuffURLS(url, &tmpbuff))
-        {
-          ajDie("Failed to download result from:\n%S\n", url);
-        }
-
-      ajBuffreadLine(tmpbuff, &tmp);
-
-      parse = ajStrNew();
-      gcsi  = ajStrNew();
-      sa    = ajStrNew();
-      dist  = ajStrNew();
-      z     = ajStrNew();
-      p     = ajStrNew();
-
-      ajStrRemoveLastNewline(&tmp);
-
-      handle = ajStrTokenNewC(tmp, ",");
-
-      while (ajStrTokenNextParse(handle, &parse))
-        {
-          if (ajStrIsFloat(parse))
-            {
-              if(!ajStrGetLen(gcsi))
-                ajStrAssignS(&gcsi, parse);
-              else if(!ajStrGetLen(sa))
-                ajStrAssignS(&sa, parse);
-              else if(!ajStrGetLen(dist))
-                ajStrAssignS(&dist, parse);
-              else if(!ajStrGetLen(z))
-                ajStrAssignS(&z, parse);
-              else if(!ajStrGetLen(p))
-                ajStrAssignS(&p, parse);
-            }
-        }
-
-      tmp = ajFmtStr("Sequence: %S GCSI: %S SA: %S DIST: %S",
-                     seqid, gcsi, sa, dist);
-
-      if(pval)
-        tmp = ajFmtStr("%S Z: %S P: %S", tmp, z, p);
-
-      ajFmtPrintF(outf, "%S\n", tmp);
-
-      ajStrDel(&tmp);
-      ajStrDel(&parse);
-      ajStrDel(&gcsi);
-      ajStrDel(&sa);
-      ajStrDel(&dist);
-      ajStrDel(&z);
-      ajStrDel(&p);
-
-      ajStrDel(&inseq);
-    }
-
-  ajFileClose(&outf);
-
-  ajSeqallDel(&seqall);
-  ajSeqDel(&seq);
-  ajStrDel(&seqid);
-
-  embExit();
-
-  return 0;
-}