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1 /******************************************************************************
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2 ** @source ggcwin
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3 **
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4 ** Calculates the GC content along the given genome
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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 RESTify
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11 ** @modified 2015/2/7 Refactor
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12 ** @@
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13 **
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14 ** This program is free software; you can redistribute it and/or
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15 ** modify it under the terms of the GNU General Public License
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16 ** as published by the Free Software Foundation; either version 2
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17 ** of the License, or (at your option) any later version.
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18 **
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19 ** This program is distributed in the hope that it will be useful,
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20 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
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21 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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22 ** GNU General Public License for more details.
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23 **
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24 ** You should have received a copy of the GNU General Public License
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25 ** along with this program; if not, write to the Free Software
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26 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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27 ******************************************************************************/
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28
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29 #include "emboss.h"
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30 #include "glibs.h"
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31
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32
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33
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34
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35 /* @prog ggcwin ***************************************************************
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36 **
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37 ** Calculates the GC content along the given genome
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38 **
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39 ******************************************************************************/
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40
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41 int main(int argc, char *argv[])
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42 {
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43 embInitPV("ggcwin", argc, argv, "GEMBASSY", "1.0.3");
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44
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45 AjPSeqall seqall;
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46 AjPSeq seq;
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47 AjPStr inseq = NULL;
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48
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49 AjBool accid = ajFalse;
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50 AjPStr restid = NULL;
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51 AjPStr seqid = NULL;
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52
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53 AjPStr base = NULL;
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54 AjPStr url = NULL;
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55
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56 AjPStr tmpname = NULL;
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57 AjPSeqout tmpout = NULL;
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58
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59 ajint window = 0;
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60 AjBool at = 0;
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61 AjBool purine = 0;
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62 AjBool keto = 0;
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63
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64 AjBool plot = 0;
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65 AjPFile outf = NULL;
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66 AjPFilebuff buff = NULL;
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67 AjPGraph mult = NULL;
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68
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69 gPlotParams gpp;
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70 AjPStr title = NULL;
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71
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72 seqall = ajAcdGetSeqall("sequence");
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73 window = ajAcdGetInt("window");
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74 at = ajAcdGetBoolean("at");
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75 purine = ajAcdGetBoolean("purine");
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76 keto = ajAcdGetBoolean("keto");
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77
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78 plot = ajAcdGetToggle("plot");
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79 outf = ajAcdGetOutfile("outfile");
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80 mult = ajAcdGetGraphxy("graph");
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81
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82 base = ajStrNewC("rest.g-language.org");
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83
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84 gAssignUniqueName(&tmpname);
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85 ajStrAppendC(&tmpname, ".fasta");
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86
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87 while(ajSeqallNext(seqall, &seq))
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88 {
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89 tmpout = ajSeqoutNew();
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90
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91 if(!ajSeqoutOpenFilename(tmpout, tmpname))
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92 {
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93 embExitBad();
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94 }
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95
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96 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
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97 ajSeqoutWriteSeq(tmpout, seq);
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98 ajSeqoutClose(tmpout);
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99 ajSeqoutDel(&tmpout);
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100
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101 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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102 gFilePostSS(url, tmpname, &restid);
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103 ajStrDel(&url);
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104 ajSysFileUnlinkS(tmpname);
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105
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106 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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107
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108 if(ajStrGetLen(seqid) == 0)
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109 {
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110 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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111 }
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112
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113 if(ajStrGetLen(seqid) == 0)
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114 {
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115 ajWarn("No valid header information\n");
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116 }
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117
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118 url = ajStrNew();
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119
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120 ajFmtPrintS(&url, "http://%S/%S/gcwin/window=%d/at=%d/purine=%d/"
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121 "keto=%d/output=f/", base, restid, window, at, purine, keto);
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122
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123 if(plot)
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124 {
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125 title = ajStrNew();
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126
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127 ajStrAppendC(&title, argv[0]);
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128 ajStrAppendC(&title, " of ");
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129 ajStrAppendS(&title, seqid);
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130
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131 gpp.title = ajStrNewS(title);
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132 gpp.xlab = ajStrNewC("location");
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133 gpp.ylab = ajStrNewC("GC content");
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134
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135 if(!gFilebuffURLS(url, &buff))
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136 {
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137 ajDie("File downloading error from:\n%S\n", url);
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138 }
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139
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140 if(!gPlotFilebuff(buff, mult, &gpp))
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141 {
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142 ajDie("Error in plotting\n");
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143 }
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144
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145 AJFREE(gpp.title);
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146 AJFREE(gpp.xlab);
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147 AJFREE(gpp.ylab);
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148 ajStrDel(&title);
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149 ajFilebuffDel(&buff);
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150 }
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151 else
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152 {
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153 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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154 if(!gFileOutURLS(url, &outf))
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155 {
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156 ajDie("File downloading error from:\n%S\n", url);
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157 }
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158 }
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159 ajStrDel(&url);
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160 ajStrDel(&restid);
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161 ajStrDel(&seqid);
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162 }
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163
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164 ajFileClose(&outf);
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165
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166 ajSeqallDel(&seqall);
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167 ajSeqDel(&seq);
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168 ajStrDel(&base);
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169
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170 embExit();
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171
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172 return 0;
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173 }
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