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1 /******************************************************************************
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2 ** @source goligomersearch
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3 **
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4 ** Counts the number of given oligomers in a sequence
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5 **
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6 ** @author Copyright (C) 2012 Hidetoshi Itaya
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7 ** @version 1.0.3
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8 ** @modified 2012/1/20 Hidetoshi Itaya Created!
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9 ** @modified 2013/6/16 Revision 1
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10 ** @modified 2015/2/7 Refactor
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11 ** @@
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12 **
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13 ** This program is free software; you can redistribute it and/or
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14 ** modify it under the terms of the GNU General Public License
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15 ** as published by the Free Software Foundation; either version 2
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16 ** of the License, or (at your option) any later version.
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17 **
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18 ** This program is distributed in the hope that it will be useful,
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19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
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20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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21 ** GNU General Public License for more details.
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22 **
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23 ** You should have received a copy of the GNU General Public License
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24 ** along with this program; if not, write to the Free Software
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25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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26 ******************************************************************************/
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27
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28 #include "emboss.h"
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29 #include "glibs.h"
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30
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31
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32
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33
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34 /* @prog goligomersearch ******************************************************
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35 **
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36 ** Counts the number of given oligomers in a sequence
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37 **
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38 ******************************************************************************/
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39
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40 int main(int argc, char *argv[])
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41 {
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42 embInitPV("goligomersearch", argc, argv, "GEMBASSY", "1.0.3");
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43
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44 AjPSeqall seqall;
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45 AjPSeq seq;
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46 AjPStr inseq = NULL;
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47 AjPStr oligomer = NULL;
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48
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49 AjPStr restid = NULL;
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50 AjPStr seqid = NULL;
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51
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52 AjPStr base = NULL;
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53 AjPStr url = NULL;
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54
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55 AjPStr _return = NULL;
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56
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57 AjPStr tmpname = NULL;
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58 AjPSeqout tmpout = NULL;
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59
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60 AjPFilebuff tmp = NULL;
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61 AjPStr line = NULL;
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62
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63 AjPFile outfile = NULL;
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64
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65 seqall = ajAcdGetSeqall("sequence");
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66 oligomer = ajAcdGetString("oligomer");
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67 _return = ajAcdGetSelectSingle("return");
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68 outfile = ajAcdGetOutfile("outfile");
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69
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70 base = ajStrNewC("rest.g-language.org");
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71
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72 gAssignUniqueName(&tmpname);
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73 ajStrAppendC(&tmpname, ".fasta");
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74
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75 while(ajSeqallNext(seqall, &seq))
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76 {
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77 inseq = NULL;
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78
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79 tmpout = ajSeqoutNew();
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80
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81 if(!ajSeqoutOpenFilename(tmpout, tmpname))
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82 {
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83 embExitBad();
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84 }
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85
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86 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
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87 ajSeqoutWriteSeq(tmpout, seq);
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88 ajSeqoutClose(tmpout);
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89 ajSeqoutDel(&tmpout);
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90
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91 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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92 gFilePostSS(url, tmpname, &restid);
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93 ajStrDel(&url);
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94 ajSysFileUnlinkS(tmpname);
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95
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96 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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97
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98 if(ajStrGetLen(seqid) == 0)
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99 {
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100 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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101 }
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102
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103 if(ajStrGetLen(seqid) == 0)
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104 {
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105 ajWarn("No valid header information\n");
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106 }
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107
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108 url = ajStrNew();
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109
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110 ajFmtPrintS(&url, "http://%S/%S/oligomer_search/%S/return=%S",
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111 base, restid, oligomer, _return);
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112
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113 if(!gFilebuffURLS(url, &tmp))
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114 {
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115 ajDie("Failed to download result from:\n%S\n", url);
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116 }
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117
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118 ajBuffreadLine(tmp, &line);
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119
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120 ajStrRemoveSetC(&line, "\n");
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121
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122 ajFmtPrintF(outfile, "Sequence: %S Oligomer: %S Return: %S\n",
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123 seqid, oligomer, line);
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124
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125 ajStrDel(&url);
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126 ajStrDel(&restid);
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127 ajStrDel(&seqid);
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128 ajStrDel(&inseq);
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129 }
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130
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131 ajFileClose(&outfile);
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132
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133 ajSeqallDel(&seqall);
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134 ajSeqDel(&seq);
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135 ajStrDel(&base);
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136
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137 ajStrDel(&oligomer);
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138
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139 embExit();
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140
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141 return 0;
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142 }
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