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

Uploaded

--- a/GEMBASSY-1.0.3/src/greporiter.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-/******************************************************************************
-** @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;
-}