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1 /******************************************************************************
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2 ** @source gkmertable
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3 **
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4 ** Create an image showing all k-mer abundance within a sequence
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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 "soapH.h"
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30 #include "GLANGSoapBinding.nsmap"
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31 #include "soapClient.c"
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32 #include "soapC.c"
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33 #include "../gsoap/stdsoap2.c"
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34 #include "glibs.h"
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35
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36
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37
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38
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39 /* @prog gkmertable ***********************************************************
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40 **
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41 ** Create an image showing all k-mer abundance within a sequence
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42 **
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43 ******************************************************************************/
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44
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45 int main(int argc, char *argv[])
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46 {
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47 embInitPV("gkmertable", argc, argv, "GEMBASSY", "1.0.3");
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48
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49 struct soap soap;
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50 struct ns1__kmer_USCOREtableInputParams params;
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51
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52 AjPSeqall seqall;
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53 AjPSeq seq;
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54 AjPStr inseq = NULL;
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55 AjPStr seqid = NULL;
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56 ajint k = 0;
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57 AjBool accid = ajFalse;
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58 AjPFile outf = NULL;
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59 AjPStr filename = NULL;
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60 AjPStr outfname = NULL;
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61 AjPStr format = NULL;
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62
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63 ajint i;
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64
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65 char *in0;
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66 char *result;
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67
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68 seqall = ajAcdGetSeqall("sequence");
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69 k = ajAcdGetInt("k");
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70 filename = ajAcdGetString("goutfile");
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71 format = ajAcdGetString("format");
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72
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73 params.k = k;
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74
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75 i = 0;
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76
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77 while(ajSeqallNext(seqall, &seq))
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78 {
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79
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80 soap_init(&soap);
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81
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82 inseq = NULL;
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83
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84 ajStrAppendC(&inseq, ">");
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85 ajStrAppendS(&inseq, ajSeqGetAccS(seq));
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86 ajStrAppendC(&inseq, "\n");
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87 ajStrAppendS(&inseq, ajSeqGetSeqS(seq));
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88
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89 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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90
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91 in0 = ajCharNewS(inseq);
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92
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93 if(soap_call_ns1__kmer_USCOREtable(
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94 &soap,
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95 NULL,
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96 NULL,
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97 in0,
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98 ¶ms,
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99 &result
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100 ) == SOAP_OK)
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101 {
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102 ++i;
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103
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104 outfname = ajStrNewS(ajFmtStr("%S.%d.%S",
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105 filename,
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106 i,
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107 format));
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108
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109 outf = ajFileNewOutNameS(outfname);
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110
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111 if(!outf)
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112 {
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113 ajDie("File open error\n");
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114 }
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115
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116 if(!ajStrMatchC(format, "png"))
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117 {
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118 if(!gHttpConvertC(result, &outf, ajStrNewC("png"), format))
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119 {
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120 ajDie("File downloading error from:\n%s\n", result);
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121 }
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122 else
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123 {
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124 ajFmtPrint("Created %S\n", outfname);
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125 }
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126 }
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127 else
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128 {
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129 if(!gHttpGetBinC(result, &outf))
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130 {
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131 ajDie("File downloading error from:\n%s\n", result);
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132 }
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133 else
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134 {
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135 ajFmtPrint("Created %S\n", outfname);
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136 }
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137 }
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138
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139 ajStrDel(&outfname);
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140 }
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141 else
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142 {
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143 soap_print_fault(&soap, stderr);
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144 }
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145
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146 soap_destroy(&soap);
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147 soap_end(&soap);
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148 soap_done(&soap);
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149
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150 AJFREE(in0);
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151
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152 ajStrDel(&seqid);
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153 ajStrDel(&inseq);
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154 }
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155
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156 ajSeqallDel(&seqall);
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157 ajSeqDel(&seq);
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158
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159 ajStrDel(&filename);
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160
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161 embExit();
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162
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163 return 0;
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164 }
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