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1 /******************************************************************************
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2 ** @source gcbi
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3 **
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4 ** Calculates the codon bias index
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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 gcbi *****************************************************************
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35 **
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36 ** Calculates the codon bias index
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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("gcbi", 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 AjBool translate = ajFalse;
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49 AjPStr delkey = NULL;
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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 AjPFile outf = NULL;
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62
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63 seqall = ajAcdGetSeqall("sequence");
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64 translate = ajAcdGetBoolean("translate");
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65 delkey = ajAcdGetString("delkey");
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66 accid = ajAcdGetBoolean("accid");
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67 outf = ajAcdGetOutfile("outfile");
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68
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69 base = ajStrNewC("rest.g-language.org");
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70
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71 gAssignUniqueName(&tmpname);
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72
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73 while(ajSeqallNext(seqall, &seq))
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74 {
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75 inseq = NULL;
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76
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77 if(!accid)
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78 {
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79 if(gFormatGenbank(seq, &inseq))
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80 {
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81 tmpfile = ajFileNewOutNameS(tmpname);
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82 if(!tmpfile)
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83 {
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84 ajDie("Output file (%S) open error\n", tmpname);
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85 }
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86 ajFmtPrintF(tmpfile, "%S", inseq);
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87 ajFileClose(&tmpfile);
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88 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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89 gFilePostSS(url, tmpname, &restid);
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90 ajStrDel(&url);
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91 ajSysFileUnlinkS(tmpname);
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92 }
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93 else
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94 {
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95 ajWarn("Sequence does not have features\n"
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96 "Proceeding with sequence accession ID\n");
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97 accid = ajTrue;
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98 }
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99 }
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100
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101 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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102
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103 if(ajStrGetLen(seqid) == 0)
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104 {
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105 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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106 }
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107
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108 if(ajStrGetLen(seqid) == 0)
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109 {
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110 ajWarn("No valid header information\n");
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111 }
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112
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113 if(accid)
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114 {
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115 ajStrAssignS(&restid, seqid);
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116 if(ajStrGetLen(seqid) == 0)
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117 {
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118 ajDie("Cannot proceed without header with -accid\n");
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119 }
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120
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121 if(!gValID(seqid))
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122 {
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123 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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124 }
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125 }
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126
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127 url = ajStrNew();
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128
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129 ajFmtPrintS(&url, "http://%S/%S/cbi/translate=%d/delkey=%S/"
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130 "output=f/tag=gene", base, restid, translate, delkey);
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131
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132 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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133 if(!gFileOutURLS(url, &outf))
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134 {
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135 ajDie("Failed to download result from:\n%S\n", url);
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136 }
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137
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138 ajStrDel(&url);
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139 ajStrDel(&restid);
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140 ajStrDel(&seqid);
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141 ajStrDel(&inseq);
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142 }
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143
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144 ajFileClose(&outf);
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145
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146 ajSeqallDel(&seqall);
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147 ajSeqDel(&seq);
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148 ajStrDel(&base);
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149
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150 ajStrDel(&delkey);
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151
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152 embExit();
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153
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154 return 0;
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155 }
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