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1 /******************************************************************************
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2 ** @source gquerystrand
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3 **
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4 ** Get the strand name (leading or lagging) from the given position
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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 gquerystrand *********************************************************
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36 **
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37 ** Get the strand name (leading or lagging) from the given position
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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("gquerystrand", 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 AjPStr inseq = NULL;
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48
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49 AjBool accid = ajFalse;
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50 AjPStr restid = NULL;
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51 AjPStr seqid = NULL;
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52
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53 AjPStr base = NULL;
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54 AjPStr url = NULL;
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55
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56 ajint position = 0;
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57 AjPStr direction = 0;
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58
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59 AjPFile outf = 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 AjPFilebuff tmp = NULL;
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65 AjPStr line = NULL;
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66
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67 seqall = ajAcdGetSeqall("sequence");
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68 position = ajAcdGetInt("position");
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69 direction = ajAcdGetSelectSingle("direction");
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70 accid = ajAcdGetBoolean("accid");
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71 outf = ajAcdGetOutfile("outfile");
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72
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73 base = ajStrNewC("rest.g-language.org");
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74
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75 gAssignUniqueName(&tmpname);
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76
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77 while(ajSeqallNext(seqall, &seq))
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78 {
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79 inseq = NULL;
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80
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81 if(!accid)
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82 {
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83 if(gFormatGenbank(seq, &inseq))
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84 {
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85 tmpfile = ajFileNewOutNameS(tmpname);
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86 if(!tmpfile)
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87 {
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88 ajDie("Output file (%S) open error\n", tmpname);
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89 }
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90 ajFmtPrintF(tmpfile, "%S", inseq);
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91 ajFileClose(&tmpfile);
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92 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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93 gFilePostSS(url, tmpname, &restid);
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94 ajStrDel(&url);
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95 ajSysFileUnlinkS(tmpname);
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96 }
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97 else
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98 {
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99 ajWarn("Sequence does not have features\n"
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100 "Proceeding with sequence accession ID\n");
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101 accid = ajTrue;
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102 }
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103 }
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104
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105 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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106
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107 if(ajStrGetLen(seqid) == 0)
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108 {
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109 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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110 }
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111
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112 if(ajStrGetLen(seqid) == 0)
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113 {
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114 ajWarn("No valid header information\n");
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115 }
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116
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117 if(accid)
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118 {
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119 ajStrAssignS(&restid, seqid);
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120 if(ajStrGetLen(seqid) == 0)
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121 {
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122 ajDie("Cannot proceed without header with -accid\n");
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123 }
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124
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125 if(!gValID(seqid))
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126 {
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127 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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128 }
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129 }
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130
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131 url = ajStrNew();
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132
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133 ajFmtPrintS(&url, "http://%S/%S/query_strand/%d/direction=%S/", base,
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134 restid, position, direction);
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135
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136 if(!gFilebuffURLS(url, &tmp))
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137 {
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138 ajDie("Failed to download result from:\n%S\n", url);
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139 }
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140
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141 ajBuffreadLine(tmp, &line);
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142
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143 ajStrRemoveSetC(&line, "\n");
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144
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145 ajFmtPrintF(outf, "Sequence: %S Strand: %S\n", seqid, line);
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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 embExit();
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160
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161 return 0;
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162 }
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