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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/src/genret.c	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,302 @@
+/******************************************************************************
+** @source genret
+**
+** Retrieves various gene related infomration from genome flatfile
+**
+** @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 genret ***************************************************************
+**
+** Retrieves various gene related infomration from genome flatfile
+**
+******************************************************************************/
+
+int main(int argc, char *argv[])
+{
+  embInitPV("genret", argc, argv, "GEMBASSY", "1.0.3");
+
+  AjPSeqall seqall;
+  AjPSeq seq      = NULL;
+  AjPStr inseq    = NULL;
+  AjPStr gene     = NULL;
+  AjPStr access   = NULL;
+  AjBool accid    = ajTrue;
+  AjPStr argument = NULL;
+  AjPFile outfile = NULL;
+
+  AjPStr seqid  = NULL;
+  AjPStr restid = NULL;
+
+  AjBool valid = ajFalse;
+  AjBool isseq = ajFalse;
+  AjBool isgbk = ajFalse;
+
+  AjPFilebuff buff = NULL;
+  AjPFile  tmpfile = NULL;
+  AjPStr   tmpname = NULL;
+
+  AjPStr regexstr = NULL;
+  AjPStrTok token = NULL;
+  AjPRegexp regex = NULL;
+
+  AjPStr url  = NULL;
+  AjPStr base = NULL;
+  AjPStr head = NULL;
+  AjPStr line = NULL;
+
+  seqall   = ajAcdGetSeqall("sequence");
+  access   = ajAcdGetString("access");
+  gene     = ajAcdGetString("gene");
+  argument = ajAcdGetString("argument");
+  accid    = ajAcdGetBoolean("accid");
+  outfile  = ajAcdGetOutfile("outfile");
+
+  if(
+     ajStrMatchC(access, "translation") ||
+     ajStrMatchC(access, "get_exon") ||
+     ajStrMatchC(access, "get_exons") ||
+     ajStrMatchC(access, "get_cdsseq") ||
+     ajStrMatchC(access, "get_gbkseq") ||
+     ajStrMatchC(access, "get_geneseq") ||
+     ajStrMatchC(access, "get_intron") ||
+     ajStrMatchC(access, "getseq") ||
+     ajStrMatchC(access, "seq") ||
+     ajStrMatchC(access, "around_startcodon") ||
+     ajStrMatchC(access, "around_stopcodon") ||
+     ajStrMatchC(access, "before_startcodon") ||
+     ajStrMatchC(access, "before_stopcodon") ||
+     ajStrMatchC(access, "after_startcodon") ||
+     ajStrMatchC(access, "after_stopcodon")
+     )
+    {
+      isseq = ajTrue;
+    }
+  else if(ajStrMatchC(access, "annotate") ||
+          ajStrMatchC(access, "output"))
+    {
+      isgbk = ajTrue;
+    }
+  else
+    {
+      ajFmtPrintF(outfile, "gene,%S\n", access);
+    }
+
+  base = ajStrNewC("rest.g-language.org");
+
+  ajStrExchangeCC(&argument, " ", "/");
+  ajStrExchangeCC(&argument, ",", "/");
+  ajStrExchangeCC(&argument, "\t", "/");
+  ajStrExchangeCC(&argument, "\r", "/");
+  ajStrExchangeCC(&argument, "\n", "/");
+
+  if(ajStrMatchC(gene, "*"))
+    {
+      ajStrInsertK(&gene, 0, '.');
+    }
+
+  if(ajStrPrefixC(gene, "@") || ajStrPrefixC(gene, "list::"))
+    {
+      ajStrExchangeCC(&gene, "@", "");
+      ajStrExchangeCC(&gene, "list::", "");
+      ajStrAssignS(&tmpname, gene);
+
+      tmpfile = ajFileNewInNameS(tmpname);
+
+      if(!tmpfile)
+        {
+          ajDie("List file (%S) open error\n", tmpname);
+        }
+
+      gene = ajStrNew();
+
+      while(ajReadline(tmpfile, &line))
+        {
+          ajStrAppendS(&gene, line);
+        }
+
+      ajFileClose(&tmpfile);
+      ajStrDel(&tmpname);
+      ajStrDel(&line);
+    }
+
+  tmpname = ajStrNew();
+  gAssignUniqueName(&tmpname);
+
+  while(ajSeqallNext(seqall, &seq))
+    {
+      inseq = ajStrNew();
+
+      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
+            {
+              ajWarn("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();
+
+      if(isgbk)
+        {
+          ajFmtPrintS(&url, "http://%S/%S/%S", base, restid, access);
+        }
+      else
+        {
+          ajFmtPrintS(&url, "http://%S/%S/*/%S/%S", base, restid, access, argument);
+        }
+
+      if(!gFilebuffURLS(url, &buff))
+        {
+          ajDie("GET error from %S\n", url);
+        }
+
+      while(ajBuffreadLine(buff, &line))
+        {
+          if(isgbk){
+            ajFmtPrintF(outfile, "%S", line);
+            continue;
+          }
+
+          ajStrRemoveLastNewline(&line);
+
+          regex = ajRegCompC("^>");
+
+          if(ajRegExec(regex, line))
+            {
+              head = ajStrNew();
+
+              ajStrAssignS(&head, line);
+              ajStrTrimStartC(&head, ">");
+
+              valid = ajFalse;
+
+              token = ajStrTokenNewC(ajStrNewS(gene), " ,\t\r\n");
+
+              while(ajStrTokenNextParse(token, &regexstr))
+                {
+                  if(ajStrGetLen(regexstr))
+                    {
+                      regex = ajRegComp(regexstr);
+
+                      if(ajRegExec(regex, line))
+                        {
+                          valid = ajTrue;
+                          if(ajStrIsAlnum(regexstr))
+                            {
+                              ajStrExchangeSC(&gene, regexstr, "");
+                            }
+                        }
+
+                      ajRegFree(&regex);
+                    }
+                }
+            }
+          else
+            {
+              if(valid)
+                {
+                  if(isseq)
+                    {
+                      ajStrFmtWrap(&line, 60);
+                      ajFmtPrintF(outfile, ">%S\n%S\n", head, line);
+                    }
+                  else
+                    {
+                      ajFmtPrintF(outfile, "%S,%S\n", head, line);
+                    }
+
+                  valid = ajFalse;
+                }
+            }
+        }
+
+      ajFileClose(&outfile);
+
+      ajStrDel(&restid);
+      ajStrDel(&seqid);
+      ajStrDel(&inseq);
+    }
+
+  ajSeqallDel(&seqall);
+  ajSeqDel(&seq);
+  ajStrDel(&access);
+  ajStrDel(&gene);
+
+  embExit();
+}