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1 /******************************************************************************
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2 ** @source gcodoncompiler
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3 **
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4 ** Calculate various kinds of amino acid and codon usage data
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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 gcodoncompiler ******************************************************
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35 **
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36 ** Calculate various kinds of amino acid and codon usage data
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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("gcodoncompiler", 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 AjBool startcodon = ajFalse;
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50 AjBool stopcodon = ajFalse;
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51 AjPStr delkey = NULL;
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52 AjPStr data = 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 AjPFile outf = NULL;
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65
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66 seqall = ajAcdGetSeqall("sequence");
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67 translate = ajAcdGetBoolean("translate");
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68 startcodon = ajAcdGetBoolean("startcodon");
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69 stopcodon = ajAcdGetBoolean("stopcodon");
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70 delkey = ajAcdGetString("delkey");
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71 data = ajAcdGetListSingle("data");
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72 accid = ajAcdGetBoolean("accid");
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73 outf = ajAcdGetOutfile("outfile");
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74
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75 base = ajStrNewC("rest.g-language.org");
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76
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77 gAssignUniqueName(&tmpname);
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78
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79 while(ajSeqallNext(seqall, &seq))
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80 {
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81 inseq = NULL;
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82
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83 if(!accid)
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84 {
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85 if(gFormatGenbank(seq, &inseq))
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86 {
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87 tmpfile = ajFileNewOutNameS(tmpname);
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88 if(!tmpfile)
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89 {
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90 ajDie("Output file (%S) open error\n", tmpname);
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91 }
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92 ajFmtPrintF(tmpfile, "%S", inseq);
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93 ajFileClose(&tmpfile);
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94 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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95 gFilePostSS(url, tmpname, &restid);
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96 ajStrDel(&url);
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97 ajSysFileUnlinkS(tmpname);
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98 }
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99 else
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100 {
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101 ajWarn("Sequence does not have features\n"
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102 "Proceeding with sequence accession ID\n");
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103 accid = ajTrue;
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104 }
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105 }
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106
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107 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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108
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109 if(ajStrGetLen(seqid) == 0)
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110 {
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111 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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112 }
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113
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114 if(ajStrGetLen(seqid) == 0)
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115 {
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116 ajWarn("No valid header information\n");
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117 }
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118
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119 if(accid)
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120 {
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121 ajStrAssignS(&restid, seqid);
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122 if(ajStrGetLen(seqid) == 0)
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123 {
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124 ajDie("Cannot proceed without header with -accid\n");
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125 }
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126
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127 if(!gValID(seqid))
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128 {
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129 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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130 }
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131 }
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132
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133 url = ajStrNew();
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134
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135 ajFmtPrintS(&url, "http://%S/%S/codon_compiler//translate=%d/"
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136 "startcodon=%d/stopcodon=%d/delkey=%S/data=%S/output=f/",
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137 base, restid, translate, startcodon, stopcodon, delkey, data);
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138
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139 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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140 if(!gFileOutURLS(url, &outf))
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141 {
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142 ajDie("Failed to download result from:\n%S\n", url);
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143 }
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144
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145 ajStrDel(&url);
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146 ajStrDel(&restid);
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147 ajStrDel(&seqid);
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148 ajStrDel(&inseq);
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149 }
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150
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151 ajFileClose(&outf);
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152
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153 ajSeqallDel(&seqall);
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154 ajSeqDel(&seq);
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155 ajStrDel(&base);
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156
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157 ajStrDel(&delkey);
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158 ajStrDel(&data);
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159
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160 embExit();
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161
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162 return 0;
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163 }
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