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1 /******************************************************************************
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2 ** @source gbui
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3 **
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4 ** Calculates base usage indices for protein-coding sequences
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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 gbui ****************************************************************
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35 **
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36 ** Calculates base usage indices for protein-coding sequences
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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("gbui", 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 position = NULL;
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50 AjPStr delkey = NULL;
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51
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52 AjBool accid = ajFalse;
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53 AjPStr restid = NULL;
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54 AjPStr seqid = NULL;
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55
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56 AjPStr base = NULL;
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57 AjPStr url = NULL;
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58
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59 AjPFile tmpfile = NULL;
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60 AjPStr tmpname = NULL;
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61
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62 AjPFile outf = NULL;
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63
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64 seqall = ajAcdGetSeqall("sequence");
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65 translate = ajAcdGetBoolean("translate");
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66 position = ajAcdGetListSingle("position");
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67 delkey = ajAcdGetString("delkey");
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68 accid = ajAcdGetBoolean("accid");
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69 outf = ajAcdGetOutfile("outfile");
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70
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71 if(ajStrMatchC(position, "all"))
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72 {
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73 ajStrDel(&position);
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74 position = ajStrNew();
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75 }
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76
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77 base = ajStrNewC("rest.g-language.org");
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78
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79 gAssignUniqueName(&tmpname);
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80
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81 while(ajSeqallNext(seqall, &seq))
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82 {
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83 inseq = NULL;
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84
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85 if(!accid)
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86 {
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87 if(gFormatGenbank(seq, &inseq))
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88 {
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89 tmpfile = ajFileNewOutNameS(tmpname);
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90 if(!tmpfile)
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91 {
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92 ajDie("Output file (%S) open error\n", tmpname);
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93 }
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94 ajFmtPrintF(tmpfile, "%S", inseq);
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95 ajFileClose(&tmpfile);
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96 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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97 gFilePostSS(url, tmpname, &restid);
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98 ajStrDel(&url);
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99 ajSysFileUnlinkS(tmpname);
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100 }
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101 else
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102 {
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103 ajWarn("Sequence does not have features\n"
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104 "Proceeding with sequence accession ID\n");
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105 accid = ajTrue;
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106 }
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107 }
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108
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109 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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110
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111 if(ajStrGetLen(seqid) == 0)
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112 {
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113 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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114 }
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115
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116 if(ajStrGetLen(seqid) == 0)
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117 {
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118 ajWarn("No valid header information\n");
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119 }
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120
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121 if(accid)
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122 {
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123 ajStrAssignS(&restid, seqid);
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124 if(ajStrGetLen(seqid) == 0)
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125 {
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126 ajDie("Cannot proceed without header with -accid\n");
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127 }
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128
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129 if(!gValID(seqid))
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130 {
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131 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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132 }
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133 }
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134
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135 url = ajStrNew();
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136
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137 ajFmtPrintS(&url, "http://%S/%S/bui/translate=%d/position=%S/"
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138 "delkey=%S/output=f/tag=gene", base, restid, translate,
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139 position, delkey);
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140
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141 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
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142 if(!gFileOutURLS(url, &outf))
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143 {
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144 ajDie("Failed to download result from:\n%S\n", url);
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145 }
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146
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147 ajStrDel(&url);
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148 ajStrDel(&restid);
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149 ajStrDel(&seqid);
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150 ajStrDel(&inseq);
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151 }
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152
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153 ajFileClose(&outf);
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154
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155 ajSeqallDel(&seqall);
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156 ajSeqDel(&seq);
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157 ajStrDel(&base);
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158
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159 ajStrDel(&position);
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160 ajStrDel(&delkey);
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161
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162 embExit();
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163
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164 return 0;
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165 }
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