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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/gfindoriter.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,167 @@
+/******************************************************************************
+** @source gfindoriter
+**
+** Predict the replication origin and terminus in bacterial genomes
+**
+** @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 gfindoriter ********************************************************
+**
+** Predict the replication origin and terminus in bacterial genomes
+**
+******************************************************************************/
+
+int main(int argc, char *argv[])
+{
+  embInitPV("gfindoriter", argc, argv, "GEMBASSY", "1.0.3");
+
+  AjPSeqall seqall;
+  AjPSeq    seq;
+
+  ajint	 window  = 0;
+  AjBool purine  = 0;
+  AjBool keto    = 0;
+  ajint	 lowpass = 0;
+
+  AjPStr ori = NULL;
+  AjPStr ter = NULL;
+
+  AjPStr restid = NULL;
+  AjPStr seqid  = NULL;
+
+  AjPStr base = NULL;
+  AjPStr url  = NULL;
+
+  AjPStr      tmpname = NULL;
+  AjPSeqout   tmpout  = NULL;
+  AjPFilebuff tmpbuff = NULL;
+
+  AjPStr tmp  = NULL;
+  AjPStr line = NULL;
+
+  AjPRegexp regex;
+
+  AjPFile outf = NULL;
+
+  seqall = ajAcdGetSeqall("sequence");
+  window = ajAcdGetInt("window");
+  lowpass = ajAcdGetInt("lowpass");
+  purine = ajAcdGetBoolean("purine");
+  keto   = ajAcdGetBoolean("keto");
+  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/find_ori_ter/window=%d/lowpass=%d/"
+                  "purine=%d/keto=%d/", base, restid, window, lowpass,
+                  purine, keto);
+
+      if(!gFilebuffURLS(url, &tmpbuff))
+        {
+          ajDie("Failed to download result from:\n%S\n", url);
+        }
+
+      regex = ajRegCompC("([0-9]+)$");
+
+      while(ajBuffreadLine(tmpbuff, &line))
+        {
+          if(ajRegExec(regex, line))
+            {
+              if(ajRegSubI(regex, 0, &tmp))
+                {
+                  if(ajStrGetLen(ori) == 0)
+                    {
+                      ajStrAssignS(&ori, tmp);
+                    }
+                  else if(ajStrGetLen(ter) == 0)
+                    {
+                      ajStrAssignS(&ter, tmp);
+                    }
+                }
+            }
+        }
+
+      ajFmtPrintF(outf, "Sequence: %S Origin: %S Terminus: %S\n",
+                  seqid, ori, ter);
+
+      ajStrDel(&tmp);
+      ajStrDel(&ori);
+      ajStrDel(&ter);
+
+      ajStrDel(&url);
+      ajStrDel(&restid);
+    }
+
+  ajFileClose(&outf);
+
+  ajSeqallDel(&seqall);
+  ajSeqDel(&seq);
+  ajStrDel(&seqid);
+
+  embExit();
+
+  return 0;
+}