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1 /******************************************************************************
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2 ** @source gfindoriter
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3 **
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4 ** Predict the replication origin and terminus in bacterial genomes
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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 gfindoriter ********************************************************
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36 **
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37 ** Predict the replication origin and terminus in bacterial genomes
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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("gfindoriter", 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
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48 ajint window = 0;
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49 AjBool purine = 0;
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50 AjBool keto = 0;
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51 ajint lowpass = 0;
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52
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53 AjPStr ori = NULL;
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54 AjPStr ter = NULL;
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55
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56 AjPStr restid = NULL;
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57 AjPStr seqid = NULL;
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58
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59 AjPStr base = NULL;
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60 AjPStr url = NULL;
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61
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62 AjPStr tmpname = NULL;
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63 AjPSeqout tmpout = NULL;
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64 AjPFilebuff tmpbuff = NULL;
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65
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66 AjPStr tmp = NULL;
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67 AjPStr line = NULL;
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68
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69 AjPRegexp regex;
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70
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71 AjPFile outf = NULL;
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72
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73 seqall = ajAcdGetSeqall("sequence");
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74 window = ajAcdGetInt("window");
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75 lowpass = ajAcdGetInt("lowpass");
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76 purine = ajAcdGetBoolean("purine");
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77 keto = ajAcdGetBoolean("keto");
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78 outf = ajAcdGetOutfile("outfile");
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79
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80 base = ajStrNewC("rest.g-language.org");
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81
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82 gAssignUniqueName(&tmpname);
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83 ajStrAppendC(&tmpname, ".fasta");
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84
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85 while(ajSeqallNext(seqall, &seq))
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86 {
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87 tmpout = ajSeqoutNew();
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88
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89 if(!ajSeqoutOpenFilename(tmpout, tmpname))
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90 {
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91 embExitBad();
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92 }
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93
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94 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
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95 ajSeqoutWriteSeq(tmpout, seq);
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96 ajSeqoutClose(tmpout);
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97 ajSeqoutDel(&tmpout);
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98
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99 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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100 gFilePostSS(url, tmpname, &restid);
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101 ajStrDel(&url);
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102 ajSysFileUnlinkS(tmpname);
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103
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104 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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105
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106 if(ajStrGetLen(seqid) == 0)
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107 {
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108 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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109 }
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110
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111 if(ajStrGetLen(seqid) == 0)
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112 {
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113 ajWarn("No valid header information\n");
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114 }
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115
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116 url = ajStrNew();
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117
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118 ajFmtPrintS(&url, "http://%S/%S/find_ori_ter/window=%d/lowpass=%d/"
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119 "purine=%d/keto=%d/", base, restid, window, lowpass,
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120 purine, keto);
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121
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122 if(!gFilebuffURLS(url, &tmpbuff))
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123 {
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124 ajDie("Failed to download result from:\n%S\n", url);
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125 }
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126
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127 regex = ajRegCompC("([0-9]+)$");
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128
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129 while(ajBuffreadLine(tmpbuff, &line))
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130 {
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131 if(ajRegExec(regex, line))
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132 {
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133 if(ajRegSubI(regex, 0, &tmp))
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134 {
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135 if(ajStrGetLen(ori) == 0)
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136 {
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137 ajStrAssignS(&ori, tmp);
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138 }
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139 else if(ajStrGetLen(ter) == 0)
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140 {
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141 ajStrAssignS(&ter, tmp);
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142 }
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143 }
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144 }
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145 }
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146
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147 ajFmtPrintF(outf, "Sequence: %S Origin: %S Terminus: %S\n",
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148 seqid, ori, ter);
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149
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150 ajStrDel(&tmp);
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151 ajStrDel(&ori);
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152 ajStrDel(&ter);
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153
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154 ajStrDel(&url);
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155 ajStrDel(&restid);
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156 }
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157
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158 ajFileClose(&outf);
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159
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160 ajSeqallDel(&seqall);
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161 ajSeqDel(&seq);
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162 ajStrDel(&seqid);
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163
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164 embExit();
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165
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166 return 0;
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167 }
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