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

Uploaded

--- a/GEMBASSY-1.0.3/src/genret.c	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,302 +0,0 @@
-/******************************************************************************
-** @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();
-}