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1 /******************************************************************************
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2 ** @source gviewcds
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3 **
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4 ** Displays a graph of nucleotide contents around start and stop codons
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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 gviewcds ************************************************************
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35 **
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36 ** Displays a graph of nucleotide contents around start and stop codons
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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("gviewcds", 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
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48 ajint length = 0;
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49 ajint gap = 0;
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50
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51 AjBool accid = ajFalse;
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52 AjPStr restid = NULL;
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53 AjPStr seqid = NULL;
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54
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55 AjPStr base = NULL;
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56 AjPStr url = NULL;
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57
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58 AjPFile tmpfile = NULL;
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59 AjPStr tmpname = NULL;
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60
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61 AjBool plot = 0;
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62 AjPFile outf = NULL;
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63 AjPFilebuff buff = NULL;
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64 AjPGraph mult = NULL;
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65
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66 gPlotParams gpp;
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67 AjPStr title = NULL;
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68 AjPPStr names = NULL;
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69
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70 ajint i;
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71
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72 seqall = ajAcdGetSeqall("sequence");
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73 length = ajAcdGetInt("length");
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74 gap = ajAcdGetInt("gap");
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75 accid = ajAcdGetBoolean("accid");
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76
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77 plot = ajAcdGetToggle("plot");
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78 outf = ajAcdGetOutfile("outfile");
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79 mult = ajAcdGetGraphxy("graph");
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80
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81 base = ajStrNewC("rest.g-language.org");
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82
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83 gAssignUniqueName(&tmpname);
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84
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85 while(ajSeqallNext(seqall, &seq))
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86 {
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87 inseq = NULL;
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88
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89 if(!accid)
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90 {
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91 if(gFormatGenbank(seq, &inseq))
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92 {
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93 gAssignUniqueName(&tmpname);
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94
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95 tmpfile = ajFileNewOutNameS(tmpname);
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96
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97 if(!tmpfile)
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98 {
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99 ajFmtError("Output file (%S) open error\n", tmpname);
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100 embExitBad();
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101 }
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102
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103 ajFmtPrintF(tmpfile, "%S", inseq);
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104 ajFileClose(&tmpfile);
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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 else
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111 {
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112 ajFmtError("Sequence does not have features\n"
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113 "Proceeding with sequence accession ID\n");
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114 accid = ajTrue;
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115 }
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116 }
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117
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118 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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119
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120 if(ajStrGetLen(seqid) == 0)
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121 {
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122 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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123 }
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124
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125 if(ajStrGetLen(seqid) == 0)
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126 {
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127 ajWarn("No valid header information\n");
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128 }
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129
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130 if(accid)
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131 {
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132 ajStrAssignS(&restid, seqid);
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133 if(ajStrGetLen(seqid) == 0)
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134 {
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135 ajDie("Cannot proceed without header with -accid\n");
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136 }
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137
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138 if(!gValID(seqid))
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139 {
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140 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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141 }
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142 }
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143
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144 url = ajStrNew();
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145
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146 ajFmtPrintS(&url, "http://%S/%S/view_cds/length=%d/gap=%d/"
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147 "output=f/tag=gene", base, restid, length, gap);
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148
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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("A");
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157 names[2] = ajStrNewC("T");
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158 names[3] = ajStrNewC("G");
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159 names[4] = ajStrNewC("C");
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160
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161 title = ajStrNew();
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162
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163 ajStrAppendC(&title, argv[0]);
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164 ajStrAppendC(&title, " of ");
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165 ajStrAppendS(&title, seqid);
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166
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167 gpp.title = ajStrNewS(title);
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168 gpp.xlab = ajStrNewC("position");
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169 gpp.ylab = ajStrNewC("percentage");
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170 gpp.names = names;
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171
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172 if(!gFilebuffURLS(url, &buff))
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173 {
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174 ajDie("File downloading error from:\n%S\n", url);
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175 }
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176
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177 if(!gPlotFilebuff(buff, mult, &gpp))
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178 {
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179 ajDie("Error in plotting\n");
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180 }
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181
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182 i = 0;
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183 while(names[i])
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184 {
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185 AJFREE(names[i]);
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186 ++i;
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187 }
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188
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189 AJFREE(names);
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190
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191 AJFREE(gpp.title);
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192 AJFREE(gpp.xlab);
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193 AJFREE(gpp.ylab);
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194 ajStrDel(&title);
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195 ajFilebuffDel(&buff);
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196 }
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197 else
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198 {
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199 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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200 if(!gFileOutURLS(url, &outf))
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201 {
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202 ajDie("File downloading error from:\n%S\n", url);
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203 }
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204 }
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205 }
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206
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207 ajFileClose(&outf);
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208
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209 ajSeqallDel(&seqall);
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210 ajSeqDel(&seq);
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211 ajStrDel(&seqid);
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212
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213 embExit();
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214
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215 return 0;
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216 }
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