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1 /******************************************************************************
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2 ** @source ggcskew
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3 **
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4 ** Calculates the GC skew of the input 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 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 ggcskew **************************************************************
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36 **
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37 ** Calculates the GC skew of the input sequence
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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("ggcskew", 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 ajint slide = 0;
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61 AjBool cumulative = 0;
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62 AjBool at = 0;
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63 AjBool purine = 0;
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64 AjBool keto = 0;
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65
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66 AjBool plot = 0;
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67 AjPFile outf = NULL;
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68 AjPFilebuff buff = NULL;
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69 AjPGraph mult = NULL;
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70
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71 gPlotParams gpp;
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72 AjPStr title = NULL;
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73
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74 seqall = ajAcdGetSeqall("sequence");
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75 window = ajAcdGetInt("window");
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76 slide = ajAcdGetInt("slide");
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77 cumulative = ajAcdGetBoolean("cumulative");
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78 at = ajAcdGetBoolean("at");
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79 purine = ajAcdGetBoolean("purine");
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80 keto = ajAcdGetBoolean("keto");
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81
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82 plot = ajAcdGetToggle("plot");
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83 outf = ajAcdGetOutfile("outfile");
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84 mult = ajAcdGetGraphxy("graph");
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85
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86 base = ajStrNewC("rest.g-language.org");
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87
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88 gAssignUniqueName(&tmpname);
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89 ajStrAppendC(&tmpname, ".fasta");
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90
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91 while(ajSeqallNext(seqall, &seq))
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92 {
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93 tmpout = ajSeqoutNew();
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94
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95 if(!ajSeqoutOpenFilename(tmpout, tmpname))
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96 {
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97 embExitBad();
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98 }
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99
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100 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
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101 ajSeqoutWriteSeq(tmpout, seq);
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102 ajSeqoutClose(tmpout);
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103 ajSeqoutDel(&tmpout);
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104
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105 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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106 gFilePostSS(url, tmpname, &restid);
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107 ajStrDel(&url);
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108 ajSysFileUnlinkS(tmpname);
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109
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110 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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111
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112 if(ajStrGetLen(seqid) == 0)
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113 {
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114 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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115 }
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116
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117 if(ajStrGetLen(seqid) == 0)
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118 {
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119 ajWarn("No valid header information\n");
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120 }
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121
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122 url = ajStrNew();
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123
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124 ajFmtPrintS(&url, "http://%S/%S/gcskew/window=%d/slide=%d/cumulative=%d/"
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125 "at=%d/purine=%d/keto=%d/output=f/", base, restid, window,
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126 slide, cumulative, at, purine, keto);
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127
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128 if(plot)
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129 {
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130 title = ajStrNew();
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131
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132 ajStrAppendC(&title, argv[0]);
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133 ajStrAppendC(&title, " of ");
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134 ajStrAppendS(&title, seqid);
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135
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136 gpp.title = ajStrNewS(title);
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137 gpp.xlab = ajStrNewC("location");
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138 gpp.ylab = ajStrNewC("GC skew");
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139
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140 if(!gFilebuffURLS(url, &buff))
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141 {
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142 ajDie("File downloading error from:\n%S\n", url);
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143 }
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144
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145 if(!gPlotFilebuff(buff, mult, &gpp))
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146 {
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147 ajDie("Error in plotting\n");
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148 }
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149
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150 AJFREE(gpp.title);
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151 AJFREE(gpp.xlab);
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152 AJFREE(gpp.ylab);
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153 ajStrDel(&title);
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154 ajFilebuffDel(&buff);
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155 }
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156 else
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157 {
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158 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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159 if(!gFileOutURLS(url, &outf))
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160 {
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161 ajDie("File downloading error from:\n%S\n", url);
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162 }
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163 }
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164 ajStrDel(&url);
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165 ajStrDel(&restid);
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166 ajStrDel(&seqid);
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167 }
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168
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169 ajFileClose(&outf);
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170
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171 ajSeqallDel(&seqall);
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172 ajSeqDel(&seq);
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173 ajStrDel(&base);
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174
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175 embExit();
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176
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177 return 0;
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178 }
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