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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/greporiter.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,191 @@
+/******************************************************************************
+** @source greporiter
+**
+** Get the positions of replication origin and terminus
+**
+** @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 greporiter *********************************************************
+**
+** Get the positions of replication origin and terminus
+**
+******************************************************************************/
+
+int main(int argc, char *argv[])
+{
+  embInitPV("greporiter", argc, argv, "GEMBASSY", "1.0.3");
+
+  AjPSeqall seqall;
+  AjPSeq    seq;
+  AjPStr    inseq  = NULL;
+
+  AjBool accid  = ajFalse;
+  AjPStr restid = NULL;
+  AjPStr seqid  = NULL;
+
+  AjPStr base = NULL;
+  AjPStr url  = NULL;
+
+  AjBool oriloc = 0;
+  AjBool gcskew = 0;
+  AjBool dbonly = 0;
+  ajint	 difthreshold = 0;
+
+  AjPFile outf = NULL;
+
+  AjPFile     tmpfile = NULL;
+  AjPStr      tmpname = NULL;
+  AjPStr      fstname = NULL;
+  AjPFilebuff tmp     = NULL;
+  AjPStr      line    = NULL;
+  AjPSeqout   tmpout  = NULL;
+
+  AjPRegexp regex;
+
+  AjPStr    ori    = NULL;
+  AjPStr    ter    = NULL;
+
+  seqall = ajAcdGetSeqall("sequence");
+  difthreshold = ajAcdGetInt("difthreshold");
+  oriloc = ajAcdGetBoolean("oriloc");
+  gcskew = ajAcdGetBoolean("gcskew");
+  dbonly = ajAcdGetBoolean("dbonly");
+  accid  = ajAcdGetBoolean("accid");
+  outf   = ajAcdGetOutfile("outfile");
+
+  base = ajStrNewC("rest.g-language.org");
+
+  gAssignUniqueName(&tmpname);
+  gAssignUniqueName(&fstname);
+  ajStrAppendC(&fstname, ".fasta");
+
+  while(ajSeqallNext(seqall, &seq))
+    {
+      inseq = ajStrNew();
+
+      tmpout = ajSeqoutNew();
+
+      if(!accid)
+        {
+          if(gFormatGenbank(seq, &inseq))
+            {
+              tmpfile = ajFileNewOutNameS(tmpname);
+              if(!tmpfile)
+                {
+                  ajDie("Output file (%S) open error\n", tmpname);
+                }
+              ajFmtPrintF(tmpfile, "%S", inseq);
+              ajFileClose(&tmpfile);
+              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
+              gFilePostSS(url, tmpname, &restid);
+              ajStrDel(&url);
+              ajSysFileUnlinkS(tmpname);
+            }
+          else
+            {
+              if(!ajSeqoutOpenFilename(tmpout, fstname))
+                {
+                  embExitBad();
+                }
+
+              ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
+              ajSeqoutWriteSeq(tmpout, seq);
+              ajSeqoutClose(tmpout);
+              ajSeqoutDel(&tmpout);
+              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
+              gFilePostSS(url, fstname, &restid);
+              ajStrDel(&url);
+              ajSysFileUnlinkS(fstname);
+            }
+        }
+
+      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/rep_ori_ter/oriloc=%d/gcskew=%d/"
+                  "difthreshold=%d/dbonly=%d/",  base, restid, oriloc, gcskew,
+                  difthreshold, dbonly);
+
+      if(!gFilebuffURLS(url, &tmp))
+        {
+          ajDie("Failed to download result from:\n%S\n", url);
+        }
+
+      ajBuffreadLine(tmp, &line);
+
+      regex = ajRegCompC("([0-9]+),([0-9]+)");
+
+      if(ajRegExec(regex, line)) {
+        if(ajRegSubI(regex, 1, &ori), ajRegSubI(regex, 2, &ter)) {
+          ajFmtPrint("%S Origin: %S Terminus %S\n", seqid, ori, ter);
+        }
+      }
+
+      ajStrDel(&url);
+      ajStrDel(&restid);
+      ajStrDel(&seqid);
+      ajStrDel(&inseq);
+    }
+
+  ajFileClose(&outf);
+
+  ajSeqallDel(&seqall);
+  ajSeqDel(&seq);
+  ajStrDel(&base);
+
+  embExit();
+
+  return 0;
+}