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1 /******************************************************************************
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2 ** @source gphx
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3 **
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4 ** Identify predict highly expressed gene
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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 ** @@
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11 **
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12 ** This program is free software; you can redistribute it and/or
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13 ** modify it under the terms of the GNU General Public License
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14 ** as published by the Free Software Foundation; either version 2
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15 ** of the License, or (at your option) any later version.
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16 **
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17 ** This program is distributed in the hope that it will be useful,
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18 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
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19 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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20 ** GNU General Public License for more details.
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21 **
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22 ** You should have received a copy of the GNU General Public License
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23 ** along with this program; if not, write to the Free Software
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24 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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25 ******************************************************************************/
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26
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27 #include "emboss.h"
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28 #include "glibs.h"
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29
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30
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31
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32
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33 /* @prog gphx *****************************************************************
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34 **
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35 ** Identify predict highly expressed gene
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36 **
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37 ******************************************************************************/
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38
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39 int main(int argc, char *argv[])
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40 {
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41 embInitPV("gphx", argc, argv, "GEMBASSY", "1.0.3");
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42
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43 AjPSeqall seqall;
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44 AjPSeq seq;
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45 AjPStr inseq = NULL;
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46
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47 AjBool translate = ajFalse;
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48 AjPStr delkey = NULL;
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49
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50 AjBool accid = ajFalse;
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51 AjPStr restid = NULL;
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52 AjPStr seqid = NULL;
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53
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54 AjPStr base = NULL;
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55 AjPStr url = NULL;
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56
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57 AjPFile tmpfile = NULL;
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58 AjPStr tmpname = NULL;
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59
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60 AjPFile outf = NULL;
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61
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62 seqall = ajAcdGetSeqall("sequence");
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63 translate = ajAcdGetBoolean("translate");
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64 delkey = ajAcdGetString("delkey");
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65 accid = ajAcdGetBoolean("accid");
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66 outf = ajAcdGetOutfile("outfile");
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67
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68 base = ajStrNewC("rest.g-language.org");
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69
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70 gAssignUniqueName(&tmpname);
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71
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72 while(ajSeqallNext(seqall, &seq))
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73 {
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74 inseq = NULL;
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75
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76 if(!accid)
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77 {
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78 if(gFormatGenbank(seq, &inseq))
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79 {
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80 tmpfile = ajFileNewOutNameS(tmpname);
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81 if(!tmpfile)
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82 {
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83 ajDie("Output file (%S) open error\n", tmpname);
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84 }
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85 ajFmtPrintF(tmpfile, "%S", inseq);
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86 ajFileClose(&tmpfile);
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87 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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88 gFilePostSS(url, tmpname, &restid);
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89 ajStrDel(&url);
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90 ajSysFileUnlinkS(tmpname);
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91 }
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92 else
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93 {
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94 ajWarn("Sequence does not have features\n"
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95 "Proceeding with sequence accession ID\n");
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96 accid = ajTrue;
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97 }
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98 }
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99
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100 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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101
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102 if(ajStrGetLen(seqid) == 0)
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103 {
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104 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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105 }
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106
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107 if(ajStrGetLen(seqid) == 0)
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108 {
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109 ajWarn("No valid header information\n");
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110 }
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111
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112 if(accid)
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113 {
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114 ajStrAssignS(&restid, seqid);
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115 if(ajStrGetLen(seqid) == 0)
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116 {
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117 ajDie("Cannot proceed without header with -accid\n");
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118 }
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119
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120 if(!gValID(seqid))
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121 {
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122 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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123 }
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124 }
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125
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126 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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127
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128 url = ajStrNew();
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129
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130 ajFmtPrintS(&url, "http://%S/%S/phx/translate=%d/delkey=%S/"
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131 "output=f/tag=gene", base, restid, translate, delkey);
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132
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133 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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134 if(!gFileOutURLS(url, &outf))
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135 {
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136 ajDie("Failed to download result from:\n%S\n", url);
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137 }
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138
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139 ajStrDel(&url);
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140 ajStrDel(&restid);
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141 ajStrDel(&seqid);
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142 ajStrDel(&inseq);
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143 }
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144
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145 ajFileClose(&outf);
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146
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147 ajSeqallDel(&seqall);
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148 ajSeqDel(&seq);
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149 ajStrDel(&base);
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150
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151 ajStrDel(&delkey);
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152
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153 embExit();
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154
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155 return 0;
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156 }
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