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1 /******************************************************************************
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2 ** @source gldabias
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3 **
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4 ** Calculate strand bias of bacterial genome using linear discriminant
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5 ** analysis (LDA)
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6 **
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7 ** @author Copyright (C) 2012 Hidetoshi Itaya
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8 ** @version 1.0.3
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9 ** @modified 2012/1/20 Hidetoshi Itaya Created!
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10 ** @modified 2013/6/16 Revision 1
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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 gldabias ************************************************************
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36 **
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37 ** Calculate strand bias of bacterial genome using linear discriminant
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38 ** analysis (LDA)
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39 **
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40 ******************************************************************************/
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41
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42 int main(int argc, char *argv[])
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43 {
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44 embInitPV("gldabias", argc, argv, "GEMBASSY", "1.0.3");
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45
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46 AjPSeqall seqall;
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47 AjPSeq seq;
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48 AjPStr inseq = NULL;
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49
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50 ajint coefficients = 0;
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51 AjPStr variable = NULL;
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52
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53 AjBool accid = ajFalse;
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54 AjPStr restid = NULL;
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55 AjPStr seqid = NULL;
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56
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57 AjPStr base = NULL;
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58 AjPStr url = NULL;
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59
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60 AjPFile tmpfile = NULL;
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61 AjPStr tmpname = NULL;
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62
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63 AjPFilebuff tmp = NULL;
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64 AjPStr line = NULL;
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65
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66 AjPFile outf = NULL;
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67
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68 seqall = ajAcdGetSeqall("sequence");
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69 coefficients = ajAcdGetInt("coefficients");
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70 variable = ajAcdGetSelectSingle("variable");
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71 accid = ajAcdGetBoolean("accid");
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72 outf = ajAcdGetOutfile("outfile");
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73
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74 base = ajStrNewC("rest.g-language.org");
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75
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76 gAssignUniqueName(&tmpname);
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77
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78 while(ajSeqallNext(seqall, &seq))
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79 {
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80 inseq = NULL;
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81
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82 if(!accid)
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83 {
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84 if(gFormatGenbank(seq, &inseq))
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85 {
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86 tmpfile = ajFileNewOutNameS(tmpname);
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87 if(!tmpfile)
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88 {
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89 ajDie("Output file (%S) open error\n", tmpname);
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90 }
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91 ajFmtPrintF(tmpfile, "%S", inseq);
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92 ajFileClose(&tmpfile);
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93 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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94 gFilePostSS(url, tmpname, &restid);
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95 ajStrDel(&url);
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96 ajSysFileUnlinkS(tmpname);
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97 }
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98 else
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99 {
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100 ajWarn("Sequence does not have features\n"
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101 "Proceeding with sequence accession ID\n");
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102 accid = ajTrue;
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103 }
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104 }
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105
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106 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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107
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108 if(ajStrGetLen(seqid) == 0)
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109 {
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110 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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111 }
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112
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113 if(ajStrGetLen(seqid) == 0)
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114 {
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115 ajWarn("No valid header information\n");
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116 }
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117
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118 if(accid)
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119 {
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120 ajStrAssignS(&restid, seqid);
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121 if(ajStrGetLen(seqid) == 0)
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122 {
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123 ajDie("Cannot proceed without header with -accid\n");
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124 }
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125
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126 if(!gValID(seqid))
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127 {
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128 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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129 }
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130 }
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131
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132 url = ajStrNew();
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133
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134 ajFmtPrintS(&url, "http://%S/%S/lda_bias/coefficients=%d/variable=%S",
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135 base, restid, coefficients, variable);
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136
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137 if(!gFilebuffURLS(url, &tmp))
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138 {
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139 ajDie("Failed to download result from:\n%S\n", url);
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140 }
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141
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142 ajBuffreadLine(tmp, &line);
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143
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144 ajStrRemoveSetC(&line, "\n");
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145
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146 ajFmtPrintF(outf, "Sequence: %S LDA-BIAS: %S\n", seqid, line);
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147
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148 ajStrDel(&url);
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149 ajStrDel(&restid);
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150 ajStrDel(&seqid);
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151 ajStrDel(&inseq);
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152 }
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153
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154 ajFileClose(&outf);
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155
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156 ajSeqallDel(&seqall);
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157 ajSeqDel(&seq);
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158 ajStrDel(&base);
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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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