diff GEMBASSY-1.0.3/src/ggcsi.c @ 0:8300eb051bea draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/ggcsi.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,192 @@
+/******************************************************************************
+** @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;
+}