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1 /******************************************************************************
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2 ** @source gdeltagcskew
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3 **
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4 ** Calculates strand bias of bacterial genome using delta GC skew index
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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 gdeltagcskew ********************************************************
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35 **
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36 ** Calculates strand bias of bacterial genome using delta GC skew index
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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("gdeltagcskew", 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 at = 0;
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49 AjBool purine = 0;
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50 AjBool keto = 0;
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51 AjPStr method = 0;
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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 AjPFilebuff tmp = NULL;
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63
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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 at = ajAcdGetBoolean("at");
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70 purine = ajAcdGetBoolean("purine");
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71 keto = ajAcdGetBoolean("keto");
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72 method = ajAcdGetSelectSingle("method");
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73 accid = ajAcdGetBoolean("accid");
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74 outf = ajAcdGetOutfile("outfile");
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75
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76 base = ajStrNewC("rest.g-language.org");
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77
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78 gAssignUniqueName(&tmpname);
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79
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80 while(ajSeqallNext(seqall, &seq))
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81 {
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82 inseq = NULL;
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83
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84 if(!accid)
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85 {
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86 if(gFormatGenbank(seq, &inseq))
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87 {
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88 tmpfile = ajFileNewOutNameS(tmpname);
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89 if(!tmpfile)
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90 {
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91 ajDie("Output file (%S) open error\n", tmpname);
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92 }
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93 ajFmtPrintF(tmpfile, "%S", inseq);
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94 ajFileClose(&tmpfile);
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95 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
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96 gFilePostSS(url, tmpname, &restid);
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97 ajStrDel(&url);
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98 ajSysFileUnlinkS(tmpname);
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99 }
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100 else
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101 {
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102 ajWarn("Sequence does not have features\n"
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103 "Proceeding with sequence accession ID\n");
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104 accid = ajTrue;
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105 }
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106 }
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107
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108 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
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109
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110 if(ajStrGetLen(seqid) == 0)
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111 {
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112 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
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113 }
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114
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115 if(ajStrGetLen(seqid) == 0)
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116 {
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117 ajWarn("No valid header information\n");
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118 }
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119
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120 if(accid)
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121 {
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122 ajStrAssignS(&restid, seqid);
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123 if(ajStrGetLen(seqid) == 0)
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124 {
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125 ajDie("Cannot proceed without header with -accid\n");
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126 }
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127
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128 if(!gValID(seqid))
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129 {
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130 ajDie("Invalid accession ID:%S, exiting\n", seqid);
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131 }
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132 }
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133
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134 url = ajStrNew();
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135
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136 ajFmtPrintS(&url, "http://%S/%S/delta_gcskew/", base, restid);
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137
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138 if(!gFilebuffURLS(url, &tmp))
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139 {
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140 ajDie("Failed to download result from:\n%S\n", url);
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141 }
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142
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143 ajBuffreadLine(tmp, &line);
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144
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145 ajStrRemoveSetC(&line, "\n");
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146
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147 ajFmtPrintF(outf, "Sequence: %S DELTA-GCskew %S\n", seqid, line);
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148
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149 ajStrDel(&url);
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150 ajStrDel(&restid);
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151 ajStrDel(&seqid);
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152 ajStrDel(&inseq);
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153 }
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154
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155 ajFileClose(&outf);
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156
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157 ajSeqallDel(&seqall);
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158 ajSeqDel(&seq);
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159 ajStrDel(&base);
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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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