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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/ggeneskew.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,208 @@
+/******************************************************************************
+** @source ggeneskew
+**
+** Calculate the gene strand bias of the given genome
+**
+** @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   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 ggeneskew ************************************************************
+**
+** Calculate the gene strand bias of the given genome
+**
+******************************************************************************/
+
+int main(int argc, char *argv[])
+{
+  embInitPV("ggeneskew", argc, argv, "GEMBASSY", "1.0.3");
+
+  AjPSeqall seqall;
+  AjPSeq    seq;
+  AjPStr    inseq = NULL;
+
+  ajint	 window     = 0;
+  ajint	 slide      = 0;
+  AjBool cumulative = ajFalse;
+  AjBool gc3        = ajFalse;
+  AjPStr basetype   = NULL;
+
+  AjBool accid  = ajFalse;
+  AjPStr restid = NULL;
+  AjPStr seqid  = NULL;
+
+  AjPStr base = NULL;
+  AjPStr url  = NULL;
+
+  AjPFile tmpfile = NULL;
+  AjPStr  tmpname = NULL;
+
+  AjBool      plot = 0;
+  AjPFile     outf = NULL;
+  AjPFilebuff buff = NULL;
+  AjPGraph    mult = NULL;
+
+  gPlotParams gpp;
+  AjPStr      title = NULL;
+
+  seqall     = ajAcdGetSeqall("sequence");
+  window     = ajAcdGetInt("window");
+  slide      = ajAcdGetInt("slide");
+  cumulative = ajAcdGetBoolean("cumulative");
+  gc3        = ajAcdGetBoolean("gctri");
+  basetype   = ajAcdGetSelectSingle("base");
+  accid      = ajAcdGetBoolean("accid");
+
+  plot = ajAcdGetToggle("plot");
+  outf = ajAcdGetOutfile("outfile");
+  mult = ajAcdGetGraphxy("graph");
+
+  if(ajStrMatchC(base, "none"))
+    basetype = ajStrNewC("");
+
+  base = ajStrNewC("rest.g-language.org");
+
+  gAssignUniqueName(&tmpname);
+
+  while(ajSeqallNext(seqall, &seq))
+    {
+      inseq = NULL;
+
+      if(!accid)
+        {
+          if(gFormatGenbank(seq, &inseq))
+            {
+              gAssignUniqueName(&tmpname);
+
+              tmpfile = ajFileNewOutNameS(tmpname);
+
+              if(!tmpfile)
+                {
+                  ajFmtError("Output file (%S) open error\n", tmpname);
+                  embExitBad();
+                }
+
+              ajFmtPrintF(tmpfile, "%S", inseq);
+              ajFileClose(&tmpfile);
+              ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
+              gFilePostSS(url, tmpname, &restid);
+              ajStrDel(&url);
+              ajSysFileUnlinkS(tmpname);
+            }
+          else
+            {
+              ajFmtError("Sequence does not have features\n"
+                         "Proceeding with sequence accession ID\n");
+              accid = ajTrue;
+            }
+        }
+
+      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/geneskew/window=%d/slide=%d/"
+                  "cumulative=%d/gc3=%d/base=%S/output=f/tag=gene",
+                  base, restid, window, slide, cumulative, gc3, basetype);
+
+      if(plot)
+        {
+          title = ajStrNew();
+
+          ajStrAppendC(&title, argv[0]);
+          ajStrAppendC(&title, " of ");
+          ajStrAppendS(&title, seqid);
+
+          gpp.title = ajStrNewS(title);
+          gpp.xlab = ajStrNewC("gene skew");
+          gpp.ylab = ajStrNewC("bp");
+
+          if(!gFilebuffURLS(url, &buff))
+            {
+              ajDie("File downloading error from:\n%S\n", url);
+            }
+
+          if(!gPlotFilebuff(buff, mult, &gpp))
+            {
+              ajDie("Error in plotting\n");
+            }
+
+          AJFREE(gpp.title);
+          AJFREE(gpp.xlab);
+          AJFREE(gpp.ylab);
+          ajStrDel(&title);
+          ajFilebuffDel(&buff);
+        }
+      else
+        {
+          ajFmtPrintF(outf, "Sequence: %S\n", seqid);
+          if(!gFileOutURLS(url, &outf))
+            {
+              ajDie("File downloading error from:\n%S\n", url);
+            }
+        }
+
+      ajStrDel(&url);
+      ajStrDel(&restid);
+      ajStrDel(&seqid);
+      ajStrDel(&inseq);
+    }
+
+  ajFileClose(&outf);
+
+  ajSeqallDel(&seqall);
+  ajSeqDel(&seq);
+  ajStrDel(&base);
+
+  embExit();
+
+  return 0;
+}