Example #1
0
AjBool gFileOutURLC(char* url, AjPFile* outf){
  if(!gFileOutURLS(ajStrNewC(url), outf))
    {
      return ajFalse;
    }

  return ajTrue;
}
Example #2
0
AjBool gtaiFileOutURLS(AjPStr url, AjPFile* outf, AjBool tai){
  if(tai)
    {
      CURL *curl;
      CURLcode curl_res;

      Memory *mem = malloc(sizeof(Memory*));

      mem->size = 0;
      mem->memory = NULL;

      curl_global_init(CURL_GLOBAL_ALL);

      curl = curl_easy_init();

      if(curl)
        {
          curl_easy_setopt(curl, CURLOPT_URL, ajCharNewS(url));
          curl_easy_setopt(curl, CURLOPT_FOLLOWLOCATION, 1);
          curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, curl_write);
          curl_easy_setopt(curl, CURLOPT_WRITEDATA, mem);
        }

      curl_res = curl_easy_perform(curl);

      if(CURLE_OK == curl_res)
        {
          char* redir;
          curl_res = curl_easy_getinfo(curl, CURLINFO_EFFECTIVE_URL, &redir);

          if((CURLE_OK == curl_res) && redir) {
            ajStrAssignC(&url, redir);
            ajStrExchangeCC(&url, "cai.csv", "tai.csv");
          }
        }

      free(mem);
      curl_easy_cleanup(curl);
      curl_global_cleanup();
    }

  return gFileOutURLS(url, outf);
}
Example #3
0
int main(int argc, char *argv[])
{
  embInitPV("gp2", argc, argv, "GEMBASSY", "1.0.1");

  AjPSeqall seqall;
  AjPSeq    seq;
  AjPStr    inseq = NULL;

  AjBool accid  = ajFalse;
  AjPStr restid = NULL;
  AjPStr seqid  = NULL;

  AjPStr base = NULL;
  AjPStr url  = NULL;

  AjPFile tmpfile = NULL;
  AjPStr  tmpname = NULL;

  AjPFile outf = NULL;

  seqall = ajAcdGetSeqall("sequence");
  accid  = ajAcdGetBoolean("accid");
  outf   = ajAcdGetOutfile("outfile");

  base = ajStrNewC("rest.g-language.org");

  gAssignUniqueName(&tmpname);

  while(ajSeqallNext(seqall, &seq))
    {
      inseq = NULL;

      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
            {
              ajDie("Sequence does not have features\n"
                    "Proceeding with sequence accession ID\n");
              accid = ajTrue;
            }
        }

      if(accid)
        {
          ajStrAssignS(&restid, ajSeqGetAccS(seq));
          if(!ajStrGetLen(restid))
            {
              ajStrAssignS(&restid, ajSeqGetNameS(seq));
            }
          if(!ajStrGetLen(restid))
            {
              ajDie("No valid header information\n");
            }
        }

      ajStrAssignS(&seqid, ajSeqGetAccS(seq));

      url = ajStrNew();

      ajFmtPrintS(&url, "http://%S/%S/P2/output=f/tag=gene", base, restid);

      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
      if(!gFileOutURLS(url, &outf))
        {
          ajDie("Failed to download result from:\n%S\n", url);
        }

      ajStrDel(&url);
      ajStrDel(&inseq);
    }

  ajFileClose(&outf);

  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&seqid);

  embExit();

  return 0;
}
int main(int argc, char *argv[])
{
  embInitPV("gbaseinformationcontent", argc, argv, "GEMBASSY", "1.0.1");

  AjPSeqall seqall;
  AjPSeq    seq;
  AjPStr    inseq = NULL;

  AjPStr position   = 0;
  ajint  PatLen     = 0;
  ajint  upstream   = 0;
  ajint  downstream = 0;

  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");
  position   = ajAcdGetSelectSingle("position");
  PatLen     = ajAcdGetInt("patlen");
  upstream   = ajAcdGetInt("upstream");
  downstream = ajAcdGetInt("downstream");
  accid      = ajAcdGetBoolean("accid");

  plot = ajAcdGetToggle("plot");
  outf = ajAcdGetOutfile("outfile");
  mult = ajAcdGetGraphxy("graph");

  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;
            }
        }

      if(accid)
        {
          ajStrAssignS(&seqid, ajSeqGetAccS(seq));

          if(!ajStrGetLen(seqid))
            {
              ajStrAssignS(&seqid, ajSeqGetNameS(seq));
            }

          if(!ajStrGetLen(seqid))
            {
              ajFmtError("No valid header information\n");
              embExitBad();
            }

          ajStrAssignS(&restid, seqid);
        }

      ajStrAssignS(&seqid, ajSeqGetAccS(seq));

      url = ajStrNew();

      ajFmtPrintS(&url, "http://%S/%S/base_information_content/position=%S/"
                  "PatLen=%d/upstream=%d/downstream=%d/output=f/tag=gene",
                  base, restid, position, PatLen, upstream, downstream);

      if(plot)
        {
          title = ajStrNew();

          ajStrAppendC(&title, argv[0]);
          ajStrAppendC(&title, " of ");
          ajStrAppendS(&title, seqid);

          gpp.title = ajStrNewS(title);
          gpp.xlab = ajStrNewC("position");
          gpp.ylab = ajStrNewC("information content");

          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);
            }
        }
    }

  ajFileClose(&outf);

  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&seqid);

  ajStrDel(&position);

  embExit();

  return 0;
}
Example #5
0
int main(int argc, char *argv[])
{
    embInitPV("ggcskew", 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;

    AjPStr    tmpname = NULL;
    AjPSeqout tmpout  = NULL;

    ajint	 window     = 0;
    ajint	 slide      = 0;
    AjBool cumulative = 0;
    AjBool at         = 0;
    AjBool purine     = 0;
    AjBool keto       = 0;

    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");
    at         = ajAcdGetBoolean("at");
    purine     = ajAcdGetBoolean("purine");
    keto       = ajAcdGetBoolean("keto");

    plot = ajAcdGetToggle("plot");
    outf = ajAcdGetOutfile("outfile");
    mult = ajAcdGetGraphxy("graph");

    base = ajStrNewC("rest.g-language.org");

    gAssignUniqueName(&tmpname);
    ajStrAppendC(&tmpname, ".fasta");

    while(ajSeqallNext(seqall, &seq))
    {
        tmpout = ajSeqoutNew();

        if(!ajSeqoutOpenFilename(tmpout, tmpname))
        {
            embExitBad();
        }

        ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
        ajSeqoutWriteSeq(tmpout, seq);
        ajSeqoutClose(tmpout);
        ajSeqoutDel(&tmpout);

        ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
        gFilePostSS(url, tmpname, &restid);
        ajStrDel(&url);
        ajSysFileUnlinkS(tmpname);

        ajStrAssignS(&seqid, ajSeqGetAccS(seq));

        if(ajStrGetLen(seqid) == 0)
        {
            ajStrAssignS(&seqid, ajSeqGetNameS(seq));
        }

        if(ajStrGetLen(seqid) == 0)
        {
            ajWarn("No valid header information\n");
        }

        url = ajStrNew();

        ajFmtPrintS(&url, "http://%S/%S/gcskew/window=%d/slide=%d/cumulative=%d/"
                    "at=%d/purine=%d/keto=%d/output=f/", base, restid, window,
                    slide, cumulative, at, purine, keto);

        if(plot)
        {
            title = ajStrNew();

            ajStrAppendC(&title, argv[0]);
            ajStrAppendC(&title, " of ");
            ajStrAppendS(&title, seqid);

            gpp.title = ajStrNewS(title);
            gpp.xlab = ajStrNewC("location");
            gpp.ylab = ajStrNewC("GC skew");

            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);
    }

    ajFileClose(&outf);

    ajSeqallDel(&seqall);
    ajSeqDel(&seq);
    ajStrDel(&base);

    embExit();

    return 0;
}
Example #6
0
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;
}
Example #7
0
int main(int argc, char *argv[])
{
  embInitPV("gbasezvalue", argc, argv, "GEMBASSY", "1.0.3");

  AjPSeqall seqall;
  AjPSeq    seq;
  AjPStr    inseq = NULL;

  AjPStr position   = NULL;
  ajint	 limit      = 0;
  ajint  PatLen     = 0;
  ajint  upstream   = 0;
  ajint  downstream = 0;

  AjBool accid  = ajFalse;
  AjPStr restid = NULL;
  AjPStr seqid  = NULL;

  AjPStr base = NULL;
  AjPStr url  = NULL;

  AjPFile tmpfile = NULL;
  AjPStr  tmpname = NULL;

  AjPFile outf = NULL;

  seqall     = ajAcdGetSeqall("sequence");
  position   = ajAcdGetSelectSingle("position");
  limit      = ajAcdGetInt("limit");
  PatLen     = ajAcdGetInt("patlen");
  upstream   = ajAcdGetInt("upstream");
  downstream = ajAcdGetInt("downstream");
  accid      = ajAcdGetBoolean("accid");
  outf       = ajAcdGetOutfile("outfile");

  base = ajStrNewC("rest.g-language.org");

  gAssignUniqueName(&tmpname);

  while(ajSeqallNext(seqall, &seq))
    {
      inseq = NULL;

      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();

      ajFmtPrintS(&url, "http://%S/%S/base_z_value/position=%S/PatLen=%d"
                  "upstream=%d/downstream=%d/limit=%d/output=f/tag=gene",
                  base, restid, position, PatLen, upstream, downstream, limit);

      ajFmtPrintF(outf, "Sequence: %S\n", seqid);
      if(!gFileOutURLS(url, &outf))
        {
          ajDie("Failed to download result from:\n%S\n", url);
        }

      ajStrDel(&url);
      ajStrDel(&restid);
      ajStrDel(&seqid);
      ajStrDel(&inseq);
    }

  ajFileClose(&outf);

  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&base);

  ajStrDel(&position);

  embExit();

  return 0;
}
Example #8
0
int main(int argc, char *argv[])
{
    embInitPV("gseqinfo", argc, argv, "GEMBASSY", "1.0.3");

    AjPSeqall seqall;
    AjPSeq    seq;
    AjPStr    inseq  = NULL;

    AjPStr ori = NULL;
    AjPStr ter = NULL;

    AjPStr restid = NULL;
    AjPStr seqid  = NULL;

    AjPStr base = NULL;
    AjPStr url  = NULL;

    AjPStr      tmpname = NULL;
    AjPSeqout   tmpout  = NULL;

    AjPFile outf = NULL;

    seqall = ajAcdGetSeqall("sequence");
    outf = ajAcdGetOutfile("outfile");

    base = ajStrNewC("rest.g-language.org");

    gAssignUniqueName(&tmpname);
    ajStrAppendC(&tmpname, ".fasta");

    while(ajSeqallNext(seqall, &seq))
    {
        tmpout = ajSeqoutNew();

        if(!ajSeqoutOpenFilename(tmpout, tmpname))
        {
            embExitBad();
        }

        ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
        ajSeqoutWriteSeq(tmpout, seq);
        ajSeqoutClose(tmpout);
        ajSeqoutDel(&tmpout);

        ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
        gFilePostSS(url, tmpname, &restid);
        ajStrDel(&url);
        ajSysFileUnlinkS(tmpname);

        ajStrAssignS(&seqid, ajSeqGetAccS(seq));

        if(ajStrGetLen(seqid) == 0)
        {
            ajStrAssignS(&seqid, ajSeqGetNameS(seq));
        }

        if(ajStrGetLen(seqid) == 0)
        {
            ajWarn("No valid header information\n");
        }

        url = ajStrNew();

        ajFmtPrintS(&url, "http://%S/%S/seqinfo/", base, restid);

        ajFmtPrintF(outf, "Sequence: %S\n", seqid);
        if(!gFileOutURLS(url, &outf))
        {
            ajDie("Failed to download result from:\n%S\n", url);
        }

        ajStrDel(&url);
        ajStrDel(&restid);
        ajStrDel(&seqid);
        ajStrDel(&inseq);
    }

    ajFileClose(&outf);

    ajSeqallDel(&seqall);
    ajSeqDel(&seq);
    ajStrDel(&base);

    embExit();

    return 0;
}
int main(int argc, char *argv[])
{
  embInitPV("gviewcds", argc, argv, "GEMBASSY", "1.0.1");

  AjPSeqall seqall;
  AjPSeq    seq;
  AjPStr    inseq = NULL;

  ajint	length = 0;
  ajint	gap = 0;

  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;
  AjPPStr     names = NULL;

  ajint i;

  seqall = ajAcdGetSeqall("sequence");
  length = ajAcdGetInt("length");
  gap    = ajAcdGetInt("gap");
  accid  = ajAcdGetBoolean("accid");

  plot = ajAcdGetToggle("plot");
  outf = ajAcdGetOutfile("outfile");
  mult = ajAcdGetGraphxy("graph");

  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;
            }
        }

      if(accid)
        {
          ajStrAssignS(&seqid, ajSeqGetAccS(seq));

          if(!ajStrGetLen(seqid))
            {
              ajStrAssignS(&seqid, ajSeqGetNameS(seq));
            }

          if(!ajStrGetLen(seqid))
            {
              ajFmtError("No valid header information\n");
              embExitBad();
            }

          ajStrAssignS(&restid, seqid);
        }

      ajStrAssignS(&seqid, ajSeqGetAccS(seq));

      url = ajStrNew();

      ajFmtPrintS(&url, "http://%S/%S/view_cds/length=%d/gap=%d/"
                  "output=f/tag=gene", base, restid, length, gap);

      if(plot)
        {
          if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
            ajDie("Error in memory allocation, exiting\n");
          }

          names[0] = NULL;
          names[1] = ajStrNewC("A");
          names[2] = ajStrNewC("T");
          names[3] = ajStrNewC("G");
          names[4] = ajStrNewC("C");

          title = ajStrNew();

          ajStrAppendC(&title, argv[0]);
          ajStrAppendC(&title, " of ");
          ajStrAppendS(&title, seqid);

          gpp.title = ajStrNewS(title);
          gpp.xlab = ajStrNewC("position");
          gpp.ylab = ajStrNewC("percentage");
          gpp.names = names;

          if(!gFilebuffURLS(url, &buff))
            {
              ajDie("File downloading error from:\n%S\n", url);
            }

          if(!gPlotFilebuff(buff, mult, &gpp))
            {
              ajDie("Error in plotting\n");
            }

          i = 0;
          while(names[i])
            {
              AJFREE(names[i]);
              ++i;
            }

          AJFREE(names);

          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);
            }
        }
    }

  ajFileClose(&outf);

  ajSeqallDel(&seqall);
  ajSeqDel(&seq);
  ajStrDel(&seqid);

  embExit();

  return 0;
}