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1 /******************************************************************************
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2 ** @source ggeneskew
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3 **
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4 ** Calculate the gene strand bias 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 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 ggeneskew ************************************************************
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35 **
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36 ** Calculate the gene strand bias of the given genome
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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("ggeneskew", 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 window = 0;
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49 ajint slide = 0;
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50 AjBool cumulative = ajFalse;
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51 AjBool gc3 = ajFalse;
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52 AjPStr basetype = NULL;
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53
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54 AjBool accid = ajFalse;
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55 AjPStr restid = NULL;
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56 AjPStr seqid = NULL;
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57
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58 AjPStr base = NULL;
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59 AjPStr url = NULL;
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60
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61 AjPFile tmpfile = NULL;
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62 AjPStr tmpname = NULL;
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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 slide = ajAcdGetInt("slide");
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75 cumulative = ajAcdGetBoolean("cumulative");
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76 gc3 = ajAcdGetBoolean("gctri");
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77 basetype = ajAcdGetSelectSingle("base");
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78 accid = ajAcdGetBoolean("accid");
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79
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80 plot = ajAcdGetToggle("plot");
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81 outf = ajAcdGetOutfile("outfile");
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82 mult = ajAcdGetGraphxy("graph");
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83
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84 if(ajStrMatchC(base, "none"))
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85 basetype = ajStrNewC("");
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86
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87 base = ajStrNewC("rest.g-language.org");
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88
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89 gAssignUniqueName(&tmpname);
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90
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91 while(ajSeqallNext(seqall, &seq))
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92 {
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93 inseq = NULL;
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94
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95 if(!accid)
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96 {
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97 if(gFormatGenbank(seq, &inseq))
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98 {
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99 gAssignUniqueName(&tmpname);
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100
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101 tmpfile = ajFileNewOutNameS(tmpname);
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102
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103 if(!tmpfile)
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104 {
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105 ajFmtError("Output file (%S) open error\n", tmpname);
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106 embExitBad();
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107 }
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108
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109 ajFmtPrintF(tmpfile, "%S", inseq);
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110 ajFileClose(&tmpfile);
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111 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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112 gFilePostSS(url, tmpname, &restid);
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113 ajStrDel(&url);
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114 ajSysFileUnlinkS(tmpname);
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115 }
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116 else
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117 {
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118 ajFmtError("Sequence does not have features\n"
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119 "Proceeding with sequence accession ID\n");
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120 accid = ajTrue;
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121 }
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122 }
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123
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124 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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125
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126 if(ajStrGetLen(seqid) == 0)
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127 {
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128 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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129 }
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130
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131 if(ajStrGetLen(seqid) == 0)
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132 {
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133 ajWarn("No valid header information\n");
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134 }
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135
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136 if(accid)
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137 {
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138 ajStrAssignS(&restid, seqid);
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139 if(ajStrGetLen(seqid) == 0)
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140 {
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141 ajDie("Cannot proceed without header with -accid\n");
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142 }
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143
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144 if(!gValID(seqid))
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145 {
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146 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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147 }
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148 }
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149
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150 url = ajStrNew();
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151
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152 ajFmtPrintS(&url, "http://%S/%S/geneskew/window=%d/slide=%d/"
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153 "cumulative=%d/gc3=%d/base=%S/output=f/tag=gene",
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154 base, restid, window, slide, cumulative, gc3, basetype);
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155
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156 if(plot)
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157 {
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158 title = ajStrNew();
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159
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160 ajStrAppendC(&title, argv[0]);
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161 ajStrAppendC(&title, " of ");
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162 ajStrAppendS(&title, seqid);
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163
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164 gpp.title = ajStrNewS(title);
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165 gpp.xlab = ajStrNewC("gene skew");
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166 gpp.ylab = ajStrNewC("bp");
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167
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168 if(!gFilebuffURLS(url, &buff))
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169 {
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170 ajDie("File downloading error from:\n%S\n", url);
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171 }
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172
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173 if(!gPlotFilebuff(buff, mult, &gpp))
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174 {
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175 ajDie("Error in plotting\n");
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176 }
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177
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178 AJFREE(gpp.title);
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179 AJFREE(gpp.xlab);
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180 AJFREE(gpp.ylab);
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181 ajStrDel(&title);
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182 ajFilebuffDel(&buff);
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183 }
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184 else
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185 {
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186 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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187 if(!gFileOutURLS(url, &outf))
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188 {
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189 ajDie("File downloading error from:\n%S\n", url);
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190 }
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191 }
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192
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193 ajStrDel(&url);
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194 ajStrDel(&restid);
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195 ajStrDel(&seqid);
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196 ajStrDel(&inseq);
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197 }
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198
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199 ajFileClose(&outf);
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200
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201 ajSeqallDel(&seqall);
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202 ajSeqDel(&seq);
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203 ajStrDel(&base);
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204
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205 embExit();
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206
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207 return 0;
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208 }
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