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1 /******************************************************************************
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2 ** @source ggenomicskew
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3 **
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4 ** Calculates the GC skew in different regions of 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 ggenomicskew *********************************************************
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36 **
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37 ** Calculates the GC skew in different regions of 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("ggenomicskew", 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 ajint divide = 0;
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50 AjBool at = ajFalse;
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51
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52 AjBool accid = ajFalse;
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53 AjPStr restid = NULL;
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54 AjPStr seqid = NULL;
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55
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56 AjPStr base = NULL;
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57 AjPStr url = NULL;
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58
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59 AjPFile tmpfile = NULL;
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60 AjPStr tmpname = NULL;
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61
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62 AjBool plot = 0;
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63 AjPFile outf = NULL;
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64 AjPFilebuff buff = NULL;
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65 AjPGraph mult = NULL;
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66
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67 gPlotParams gpp;
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68 AjPStr title = NULL;
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69 AjPPStr names = NULL;
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70
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71 ajint i;
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72
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73 seqall = ajAcdGetSeqall("sequence");
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74 divide = ajAcdGetInt("divide");
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75 at = ajAcdGetBoolean("at");
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76 accid = ajAcdGetBoolean("accid");
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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
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86 while (ajSeqallNext(seqall, &seq))
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87 {
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88 inseq = NULL;
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89
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90 if(!accid)
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91 {
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92 if(gFormatGenbank(seq, &inseq))
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93 {
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94 gAssignUniqueName(&tmpname);
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95
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96 tmpfile = ajFileNewOutNameS(tmpname);
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97
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98 if(!tmpfile)
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99 {
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100 ajFmtError("Output file (%S) open error\n", tmpname);
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101 embExitBad();
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102 }
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103
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104 ajFmtPrintF(tmpfile, "%S", inseq);
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105 ajFileClose(&tmpfile);
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106 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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107 gFilePostSS(url, tmpname, &restid);
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108 ajStrDel(&url);
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109 ajSysFileUnlinkS(tmpname);
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110 }
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111 else
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112 {
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113 ajFmtError("Sequence does not have features\n"
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114 "Proceeding with sequence accession ID\n");
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115 accid = ajTrue;
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116 }
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117 }
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118
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119 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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120
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121 if(ajStrGetLen(seqid) == 0)
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122 {
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123 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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124 }
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125
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126 if(ajStrGetLen(seqid) == 0)
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127 {
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128 ajWarn("No valid header information\n");
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129 }
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130
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131 if(accid)
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132 {
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133 ajStrAssignS(&restid, seqid);
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134 if(ajStrGetLen(seqid) == 0)
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135 {
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136 ajDie("Cannot proceed without header with -accid\n");
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137 }
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138
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139 if(!gValID(seqid))
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140 {
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141 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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142 }
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143 }
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144
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145 url = ajStrNew();
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146
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147 ajFmtPrintS(&url, "http://%S/%S/genomicskew/divide=%d/at=%d/"
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148 "output=f/tag=gene", base, restid, divide, at);
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149 if(plot)
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150 {
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151 if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
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152 ajDie("Error in memory allocation, exiting\n");
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153 }
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154
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155 names[0] = NULL;
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156 names[1] = ajStrNewC("whole genome");
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157 names[2] = ajStrNewC("coding region");
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158 names[3] = ajStrNewC("intergenic region");
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159 names[4] = ajStrNewC("codon third position");
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160
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161 ajStrAppendC(&title, argv[0]);
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162 ajStrAppendC(&title, " of ");
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163 ajStrAppendS(&title, seqid);
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164
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165 gpp.title = ajStrNewS(title);
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166 gpp.xlab = ajStrNewC("location");
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167 gpp.ylab = ajStrNewC("GC skew");
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168 gpp.names = names;
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169
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170 if(!gFilebuffURLS(url, &buff))
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171 {
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172 ajDie("File downloading error from:\n%S\n", url);
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173 }
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174
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175 if(!gPlotFilebuff(buff, mult, &gpp))
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176 {
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177 ajDie("Error in plotting\n");
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178 }
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179
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180 i = 0;
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181 while(names[i])
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182 {
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183 AJFREE(names[i]);
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184 ++i;
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185 }
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186
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187 AJFREE(names);
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188
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189 ajStrDel(&title);
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190 ajStrDel(&(gpp.title));
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191 ajStrDel(&(gpp.xlab));
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192 ajStrDel(&(gpp.ylab));
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193 ajFilebuffDel(&buff);
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194 }
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195 else
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196 {
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197 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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198 if(!gFileOutURLS(url, &outf))
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199 {
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200 ajDie("File downloading error from:\n%S\n", url);
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201 }
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202 }
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203
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204 ajStrDel(&url);
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205 ajStrDel(&restid);
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206 ajStrDel(&seqid);
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207 ajStrDel(&inseq);
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208 }
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209
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210 ajFileClose(&outf);
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211
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212 ajSeqallDel(&seqall);
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213 ajSeqDel(&seq);
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214 ajStrDel(&base);
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215
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216 embExit();
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217
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218 return 0;
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219 }
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