1 | /* genabnk and Macke converting program */ |
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2 | |
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3 | #include <stdio.h> |
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4 | #include <stdlib.h> |
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5 | #include "convert.h" |
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6 | #include "global.h" |
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7 | |
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8 | extern int warning_out; |
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9 | |
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10 | /* -------------------------------------------------------------- |
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11 | * Function init_gm_data(). |
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12 | * Initialize data structure of genbank and Macke formats. |
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13 | */ |
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14 | void |
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15 | init_gm_data() { |
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16 | /* void init_macke(), init_genbank(); */ |
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17 | |
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18 | init_macke(); |
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19 | init_genbank(); |
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20 | } |
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21 | /* ---------------------------------------------------------- |
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22 | * Function genbank_to_macke(). |
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23 | * Convert from Genbank format to Macke format. |
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24 | */ |
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25 | void |
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26 | genbank_to_macke(inf, outf) |
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27 | char *inf, *outf; |
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28 | { |
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29 | FILE *IFP, *ofp; |
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30 | FILE_BUFFER ifp; |
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31 | char temp[TOKENNUM]; |
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32 | int indi, total_num; |
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33 | |
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34 | if((IFP=fopen(inf, "r"))==NULL) { |
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35 | sprintf(temp, "CANNOT open input file %s, exit.\n", inf); |
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36 | error(0, temp); |
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37 | } |
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38 | ifp = create_FILE_BUFFER(inf, IFP); |
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39 | if(Lenstr(outf) <= 0) ofp = stdout; |
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40 | else if((ofp=fopen(outf, "w"))==NULL) { |
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41 | sprintf(temp, "CANNOT open output file %s, exit.\n", outf); |
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42 | error(1, temp); |
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43 | } |
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44 | /* seq irelenvant header */ |
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45 | init(); |
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46 | init_gm_data(); |
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47 | macke_out_header(ofp); |
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48 | |
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49 | #ifdef log |
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50 | fprintf(stderr, "Start converting...\n"); |
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51 | #endif |
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52 | |
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53 | for(indi=0; indi<3; indi++) { |
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54 | FILE_BUFFER_rewind(ifp); |
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55 | init_seq_data(); |
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56 | while(genbank_in(ifp)!=EOF) { |
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57 | data.numofseq++; |
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58 | if(gtom()) { |
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59 | /* convert from genbank form to macke form */ |
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60 | switch(indi) { |
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61 | case 0: |
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62 | /* output seq display format */ |
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63 | macke_out0(ofp, GENBANK); |
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64 | break; |
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65 | case 1: |
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66 | /* output seq information */ |
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67 | macke_out1(ofp); |
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68 | break; |
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69 | case 2: |
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70 | /* output seq data */ |
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71 | macke_out2(ofp); |
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72 | break; |
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73 | default: ; |
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74 | } |
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75 | } else error(7, |
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76 | "Conversion from genbank to macke fails, Exit"); |
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77 | init_gm_data(); |
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78 | #ifdef log |
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79 | if((data.numofseq % 100)==0) |
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80 | fprintf(stderr, "%d sequences have been processed\n", |
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81 | data.numofseq); |
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82 | #endif |
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83 | } |
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84 | total_num = data.numofseq; |
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85 | if(indi==0) { |
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86 | fprintf(ofp, "#-\n"); |
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87 | /* no warning message for next loop */ |
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88 | warning_out = 0; |
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89 | } |
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90 | } /* for each seq; loop */ |
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91 | |
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92 | warning_out = 1; /* resume warning messages */ |
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93 | |
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94 | #ifdef log |
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95 | fprintf(stderr, |
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96 | "Total %d sequences have been processed\n", total_num); |
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97 | #endif |
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98 | |
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99 | } |
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100 | /* -------------------------------------------------------------- |
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101 | * Function gtom(). |
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102 | * Convert from Genbank format to Macke format. |
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103 | */ |
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104 | int |
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105 | gtom() { |
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106 | /* void genbank_key_word(), error(), Freespace(), Cpystr(); */ |
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107 | /* void Append(), gtom_remarks(), replace_entry(); */ |
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108 | /* char *Catstr(); */ |
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109 | char temp[LONGTEXT], buffer[TOKENNUM]; |
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110 | char genus[TOKENNUM], species[TOKENNUM]; |
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111 | /* char *genbank_date(), *today_date(); */ |
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112 | /* char *genbank_get_strain(), *genbank_get_subspecies(); */ |
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113 | /* char *genbank_get_atcc(); */ |
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114 | /* int Lenstr(), num_of_remark(), Cmpstr(); */ |
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115 | /* int len; */ |
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116 | /* int indj, indk, remnum; */ |
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117 | |
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118 | /* copy seq abbr, assume every entry in gbk must end with \n\0 */ |
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119 | /* no '\n' at the end of the string */ |
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120 | genbank_key_word(data.gbk.locus, 0, temp, TOKENNUM); |
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121 | replace_entry(&(data.macke.seqabbr), temp); |
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122 | |
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123 | /* copy name and definition*/ |
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124 | if(Lenstr(data.gbk.organism)>1) |
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125 | replace_entry(&(data.macke.name),data.gbk.organism); |
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126 | else if(Lenstr(data.gbk.definition)>1) { |
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127 | sscanf(data.gbk.definition, "%s %s", genus, species); |
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128 | if(species[Lenstr(species)-1]==';') |
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129 | species[Lenstr(species)-1] = '\0'; |
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130 | sprintf(temp, "%s %s\n", genus, species); |
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131 | replace_entry(&(data.macke.name), temp); |
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132 | } |
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133 | |
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134 | /* copy cc name and number */ |
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135 | if(Lenstr(data.gbk.comments.orginf.cc)>1) |
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136 | replace_entry(&(data.macke.atcc), |
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137 | data.gbk.comments.orginf.cc); |
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138 | |
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139 | /* copy rna(methods) */ |
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140 | if(Lenstr(data.gbk.comments.seqinf.methods)>1) |
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141 | replace_entry(&(data.macke.rna), |
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142 | data.gbk.comments.seqinf.methods); |
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143 | |
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144 | /* copy date---DD-MMM-YYYY\n\0 */ |
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145 | if(Lenstr(data.gbk.locus)<61) { |
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146 | data.macke.date = genbank_date(today_date()); |
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147 | Append(&(data.macke.date), "\n"); |
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148 | } else |
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149 | replace_entry(&(data.macke.date), data.gbk.locus+50); |
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150 | |
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151 | /* copy genbank entry (gbkentry has higher priority than gbk.accession)*/ |
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152 | if(Lenstr(data.gbk.comments.seqinf.gbkentry)>1) |
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153 | replace_entry(&(data.macke.acs), |
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154 | data.gbk.comments.seqinf.gbkentry); |
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155 | else { |
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156 | if(Lenstr(data.gbk.accession)>1 |
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157 | &&Cmpstr(data.gbk.accession, "No information\n")!=EQ) { |
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158 | sscanf(data.gbk.accession, "%s", buffer); |
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159 | Catstr(buffer, "\n"); |
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160 | } else Cpystr(buffer, "\n"); |
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161 | replace_entry(&(data.macke.acs), buffer); |
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162 | } |
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163 | |
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164 | /* copy the first reference from GenBank to Macke */ |
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165 | if(data.gbk.numofref>0) { |
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166 | if(Lenstr(data.gbk.reference[0].author)>1) |
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167 | replace_entry(&(data.macke.author), |
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168 | data.gbk.reference[0].author); |
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169 | |
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170 | if(Lenstr(data.gbk.reference[0].journal)>1) |
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171 | replace_entry(&(data.macke.journal), |
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172 | data.gbk.reference[0].journal); |
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173 | |
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174 | if(Lenstr(data.gbk.reference[0].title)>1) |
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175 | replace_entry(&(data.macke.title), |
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176 | data.gbk.reference[0].title); |
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177 | } /* the rest of references are put into remarks, rem:..... */ |
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178 | |
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179 | gtom_remarks(); |
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180 | |
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181 | /* adjust the strain, subspecies, and atcc information */ |
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182 | Freespace(&(data.macke.strain)); |
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183 | data.macke.strain = (char*)genbank_get_strain(); |
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184 | Freespace(&(data.macke.subspecies)); |
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185 | data.macke.subspecies = (char*)genbank_get_subspecies(); |
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186 | if(Lenstr(data.macke.atcc)<=1) { |
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187 | Freespace(&(data.macke.atcc)); |
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188 | data.macke.atcc = (char*)genbank_get_atcc(); |
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189 | } |
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190 | |
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191 | return(1); |
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192 | } |
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193 | /* -------------------------------------------------------------- |
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194 | * Function gtom_remarks(). |
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195 | * Create Macke remarks. |
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196 | */ |
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197 | void |
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198 | gtom_remarks() { |
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199 | |
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200 | int remnum, len; |
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201 | int indi, indj; |
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202 | char temp[LONGTEXT]; |
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203 | /* void gtom_copy_remark(); */ |
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204 | |
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205 | /* remarks in Macke format */ |
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206 | remnum = num_of_remark(); |
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207 | data.macke.remarks = (char**)calloc(1,(unsigned)(sizeof(char*)*remnum)); |
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208 | remnum=0; |
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209 | |
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210 | /* REFERENCE the first reference */ |
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211 | if(data.gbk.numofref>0) |
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212 | gtom_copy_remark(data.gbk.reference[0].ref, "ref:", &remnum); |
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213 | |
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214 | /* The rest of the REFERENCES */ |
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215 | for(indi=1; indi<data.gbk.numofref; indi++) { |
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216 | gtom_copy_remark(data.gbk.reference[indi].ref, "ref:", &remnum); |
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217 | gtom_copy_remark(data.gbk.reference[indi].author, "auth:", &remnum); |
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218 | gtom_copy_remark(data.gbk.reference[indi].journal, "jour:", &remnum); |
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219 | gtom_copy_remark(data.gbk.reference[indi].title, "title:", &remnum); |
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220 | gtom_copy_remark(data.gbk.reference[indi].standard, "standard:", &remnum); |
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221 | |
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222 | } /* loop for copying other reference */ |
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223 | |
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224 | /* copy keywords as remark */ |
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225 | gtom_copy_remark(data.gbk.keywords, "KEYWORDS:", &remnum); |
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226 | |
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227 | /* copy accession as remark when genbank entry also exists. */ |
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228 | gtom_copy_remark(data.gbk.accession, "GenBank ACCESSION:", &remnum); |
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229 | |
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230 | /* copy source of strain */ |
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231 | gtom_copy_remark(data.gbk.comments.orginf.source, "Source of strain:", &remnum); |
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232 | |
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233 | /* copy former name */ |
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234 | gtom_copy_remark(data.gbk.comments.orginf.formname, "Former name:", &remnum); |
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235 | |
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236 | /* copy alternate name */ |
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237 | gtom_copy_remark(data.gbk.comments.orginf.nickname, "Alternate name:", &remnum); |
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238 | |
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239 | /* copy common name */ |
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240 | gtom_copy_remark(data.gbk.comments.orginf.commname, "Common name:", &remnum); |
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241 | |
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242 | /* copy host organism */ |
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243 | gtom_copy_remark(data.gbk.comments.orginf.hostorg, "Host organism:", &remnum); |
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244 | |
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245 | /* copy RDP ID */ |
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246 | gtom_copy_remark(data.gbk.comments.seqinf.RDPid, "RDP ID:", &remnum); |
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247 | |
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248 | /* copy methods */ |
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249 | gtom_copy_remark(data.gbk.comments.seqinf.methods, "Sequencing methods:", &remnum); |
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250 | |
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251 | /* copy 3' end complete */ |
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252 | if(data.gbk.comments.seqinf.comp3!=' ') { |
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253 | if(data.gbk.comments.seqinf.comp3=='y') data.macke.remarks[remnum++] = Dupstr("3' end complete: Yes\n"); |
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254 | else data.macke.remarks[remnum++]= Dupstr("3' end complete: No\n"); |
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255 | } |
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256 | |
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257 | /* copy 5' end complete */ |
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258 | if(data.gbk.comments.seqinf.comp5!=' ') { |
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259 | if(data.gbk.comments.seqinf.comp5=='y') data.macke.remarks[remnum++]= Dupstr("5' end complete: Yes\n"); |
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260 | else data.macke.remarks[remnum++]= Dupstr("5' end complete: No\n"); |
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261 | } |
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262 | |
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263 | /* other comments, not RDP DataBase specially defined */ |
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264 | if(Lenstr(data.gbk.comments.others)>0) { |
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265 | len = Lenstr(data.gbk.comments.others); |
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266 | for(indi=0, indj=0; indi<len; indi++) |
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267 | { |
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268 | temp[indj++] = data.gbk.comments.others[indi]; |
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269 | if(data.gbk.comments.others[indi]=='\n' |
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270 | || data.gbk.comments.others[indi]=='\0') { |
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271 | temp[indj] = '\0'; |
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272 | data.macke.remarks[remnum++] = |
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273 | (char*)Dupstr(temp); |
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274 | |
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275 | indj=0; |
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276 | } /* new remark line */ |
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277 | } /* for loop to find other remarks */ |
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278 | } /* other comments */ |
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279 | |
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280 | /* done with the remarks copying */ |
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281 | |
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282 | data.macke.numofrem = remnum; |
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283 | } |
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284 | /* -------------------------------------------------------------------- |
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285 | * Function gtom_copy_remark(). |
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286 | * If string length > 1 then copy string with key to remark. |
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287 | */ |
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288 | void gtom_copy_remark(string, key, remnum) |
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289 | char *string; |
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290 | const char *key; |
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291 | int *remnum; |
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292 | { |
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293 | /* int Lenstr(); */ |
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294 | /* char *Dupstr(); */ |
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295 | /* void Append(); */ |
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296 | |
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297 | /* copy host organism */ |
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298 | if(Lenstr(string)>1) { |
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299 | data.macke.remarks[(*remnum)] |
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300 | =(char*)Dupstr(key); |
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301 | Append(&(data.macke.remarks[(*remnum)]), string); |
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302 | (*remnum)++; |
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303 | } |
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304 | } |
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305 | /* -------------------------------------------------------------------- |
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306 | * Function genbank_get_strain(). |
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307 | * Get strain from DEFINITION, COMMENT or SOURCE line in |
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308 | * Genbank data file. |
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309 | */ |
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310 | char *genbank_get_strain() { |
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311 | |
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312 | int indj, indk; |
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313 | /* int find_pattern(), Lenstr(); */ |
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314 | /* int Skip_white_space(), Reach_white_space(); */ |
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315 | char strain[LONGTEXT], temp[LONGTEXT], buffer[LONGTEXT]; |
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316 | /* void get_string(), warning(), Cpystr(); */ |
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317 | |
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318 | strain[0]='\0'; |
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319 | /* get strain */ |
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320 | if(Lenstr(data.gbk.comments.others)>1) { |
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321 | if((indj=find_pattern(data.gbk.comments.others, |
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322 | "*source:"))>=0) { |
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323 | if((indk=find_pattern( |
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324 | (data.gbk.comments.others+indj), |
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325 | "strain="))>=0) { |
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326 | /* skip blank spaces */ |
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327 | indj=Skip_white_space( |
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328 | data.gbk.comments.others, |
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329 | (indj+indk+7)); |
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330 | /* get strain */ |
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331 | get_string(data.gbk.comments.others, |
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332 | temp, indj); |
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333 | Cpystr(strain, temp); /* copy new strain */ |
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334 | } /* get strain */ |
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335 | } /* find source: line in comment */ |
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336 | } /* look for strain on comments */ |
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337 | |
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338 | if(Lenstr(data.gbk.definition)>1) { |
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339 | if((indj=find_pattern(data.gbk.definition, "str. "))>=0 |
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340 | ||(indj=find_pattern(data.gbk.definition, "strain "))>=0) { |
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341 | /* skip the key word */ |
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342 | indj=Reach_white_space(data.gbk.definition, indj); |
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343 | /* skip blank spaces */ |
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344 | indj=Skip_white_space(data.gbk.definition, indj); |
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345 | /* get strain */ |
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346 | get_string(data.gbk.definition, temp, indj); |
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347 | if(Lenstr(strain)>1) { |
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348 | if(Cmpstr(temp, strain)!=EQ){ |
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349 | sprintf(buffer, |
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350 | "Inconsistent strain definition in DEFINITION: %s and %s", |
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351 | temp, strain); |
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352 | warning(91, buffer); |
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353 | } /* check consistency of duplicated def */ |
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354 | } else Cpystr(strain, temp); /* get strain */ |
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355 | } /* find strain in definition */ |
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356 | } /* if there is definition line */ |
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357 | |
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358 | if(Lenstr(data.gbk.source)>1) { |
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359 | if((indj=find_pattern(data.gbk.source, "str. "))>=0 |
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360 | ||(indj=find_pattern(data.gbk.source, "strain "))>=0){ |
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361 | /* skip the key word */ |
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362 | indj=Reach_white_space(data.gbk.source, indj); |
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363 | /* skip blank spaces */ |
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364 | indj=Skip_white_space(data.gbk.source, indj); |
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365 | /* get strain */ |
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366 | get_string(data.gbk.source, temp, indj); |
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367 | if(Lenstr(strain)>1) { |
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368 | if(Cmpstr(temp, strain)!=EQ) { |
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369 | sprintf(buffer, |
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370 | "Inconsistent strain definition in SOURCE: %s and %s", |
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371 | temp, strain); |
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372 | warning(92, buffer); |
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373 | } |
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374 | } else Cpystr(strain, temp); |
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375 | /* check consistency of duplicated def */ |
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376 | } /* find strain */ |
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377 | } /* look for strain in SOURCE line */ |
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378 | |
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379 | return(Dupstr(strain)); |
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380 | } |
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381 | /* -------------------------------------------------------------------- |
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382 | * Function genbank_get_subspecies(). |
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383 | * Get subspecies information from SOURCE, DEFENITION, or |
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384 | * COMMENT line of Genabnk data file. |
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385 | */ |
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386 | char |
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387 | *genbank_get_subspecies() { |
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388 | |
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389 | int indj, indk; |
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390 | /* int find_pattern(), Lenstr(); */ |
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391 | /* int Skip_white_space(), Reach_white_space(); */ |
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392 | char subspecies[LONGTEXT], temp[LONGTEXT], buffer[LONGTEXT]; |
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393 | /* char *Dupstr(); */ |
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394 | /* void get_string(), warning(), Cpystr(); */ |
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395 | /* void correct_subspecies(); */ |
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396 | |
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397 | subspecies[0]='\0'; |
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398 | /* get subspecies */ |
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399 | if(Lenstr(data.gbk.definition)>1) { |
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400 | if((indj=find_pattern(data.gbk.definition, "subsp. "))>=0) { |
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401 | /* skip the key word */ |
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402 | indj=Reach_white_space(data.gbk.definition, indj); |
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403 | /* skip blank spaces */ |
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404 | indj=Skip_white_space(data.gbk.definition, indj); |
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405 | /* get subspecies */ |
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406 | get_string(data.gbk.definition, temp, indj); |
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407 | correct_subspecies(temp); |
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408 | Cpystr(subspecies, temp); |
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409 | } |
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410 | } |
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411 | if(Lenstr(data.gbk.comments.others)>1) { |
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412 | if((indj=find_pattern(data.gbk.comments.others, |
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413 | "*source:"))>=0) { |
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414 | if((indk=find_pattern((data.gbk.comments.others+indj), |
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415 | "sub-species="))>=0 |
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416 | ||(indk=find_pattern((data.gbk.comments.others+indj), |
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417 | "subspecies="))>=0 |
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418 | ||(indk=find_pattern((data.gbk.comments.others+indj), |
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419 | "subsp.="))>=0) { |
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420 | /* skip the key word */ |
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421 | for(indj+=indk; |
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422 | data.gbk.comments.others[indj]!='='; indj++); |
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423 | indj++; |
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424 | /* skip blank spaces */ |
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425 | indj=Skip_white_space(data.gbk.comments.others, indj); |
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426 | /* get subspecies */ |
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427 | get_string(data.gbk.comments.others, temp, |
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428 | indj); |
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429 | if(Lenstr(subspecies)>1){ |
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430 | if(Cmpstr(temp, subspecies)!=EQ){ |
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431 | sprintf(buffer, |
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432 | "Inconsistent subspecies definition in COMMENTS *source: %s and %s", |
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433 | temp, subspecies); |
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434 | warning(20, buffer); |
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435 | } |
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436 | } else Cpystr(subspecies, temp); |
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437 | } /* get subspecies */ |
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438 | } /* find *source: line in comment */ |
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439 | } /* look for subspecies on comments */ |
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440 | |
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441 | if(Lenstr(data.gbk.source)>1) { |
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442 | if((indj=find_pattern(data.gbk.source, "subsp. "))>=0 |
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443 | ||(indj=find_pattern(data.gbk.source, "subspecies "))>=0 |
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444 | ||(indj=find_pattern(data.gbk.source, "sub-species "))>=0) { |
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445 | /* skip the key word */ |
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446 | indj=Reach_white_space(data.gbk.source, indj); |
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447 | /* skip blank spaces */ |
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448 | indj=Skip_white_space(data.gbk.source, indj); |
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449 | /* get subspecies */ |
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450 | get_string(data.gbk.source, temp, indj); |
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451 | correct_subspecies(temp); |
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452 | if(Lenstr(subspecies)>1) { |
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453 | if(Cmpstr(temp, subspecies)!=EQ){ |
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454 | sprintf(buffer, |
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455 | "Inconsistent subspecies definition in SOURCE: %s and %s", |
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456 | temp, subspecies); |
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457 | warning(21, buffer); |
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458 | } |
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459 | } else Cpystr(subspecies, temp); |
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460 | /* check consistency of duplicated def */ |
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461 | } /* find subspecies */ |
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462 | } /* look for subspecies in SOURCE line */ |
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463 | |
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464 | return(Dupstr(subspecies)); |
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465 | } |
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466 | /* --------------------------------------------------------------- |
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467 | * Function correct_subspecies(). |
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468 | * Remove the strain information in subspecies which is |
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469 | * sometime mistakenly written into it. |
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470 | */ |
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471 | void |
---|
472 | correct_subspecies(subspecies) |
---|
473 | char *subspecies; |
---|
474 | { |
---|
475 | int indj; |
---|
476 | |
---|
477 | if((indj=find_pattern(subspecies, "str\n"))>=0 |
---|
478 | ||(indj=find_pattern(subspecies, "str."))>=0 |
---|
479 | ||(indj=find_pattern(subspecies, "strain"))>=0) { |
---|
480 | subspecies[indj-1]='\n'; |
---|
481 | subspecies[indj]='\0'; |
---|
482 | } |
---|
483 | } |
---|
484 | /* -------------------------------------------------------------------- |
---|
485 | * Function genbank_get_atcc(). |
---|
486 | * Get atcc from SOURCE line in Genbank data file. |
---|
487 | */ |
---|
488 | char |
---|
489 | *genbank_get_atcc() { |
---|
490 | |
---|
491 | /* int Lenstr(); */ |
---|
492 | char temp[LONGTEXT]; |
---|
493 | char *atcc; |
---|
494 | |
---|
495 | |
---|
496 | atcc = NULL; |
---|
497 | /* get culture collection # */ |
---|
498 | if(Lenstr(data.gbk.source)>1) |
---|
499 | atcc = get_atcc(data.gbk.source); |
---|
500 | if(Lenstr(atcc)<=1&&Lenstr(data.macke.strain)>1) { |
---|
501 | /* add () to macke strain to be processed correctly */ |
---|
502 | sprintf(temp, "(%s)", data.macke.strain); |
---|
503 | atcc = get_atcc(temp); |
---|
504 | } |
---|
505 | return(atcc); |
---|
506 | } |
---|
507 | /* ------------------------------------------------------------------- */ |
---|
508 | /* Function get_atcc(). |
---|
509 | */ |
---|
510 | char |
---|
511 | *get_atcc(source) |
---|
512 | char *source; |
---|
513 | { |
---|
514 | |
---|
515 | static int cc_num=16; |
---|
516 | static const char *CC[16] = {"ATCC", "CCM", "CDC", "CIP", "CNCTC", |
---|
517 | "DSM", "EPA", "JCM", "NADC", "NCDO", "NCTC", "NRCC", |
---|
518 | "NRRL", "PCC", "USDA", "VPI"}; |
---|
519 | /* int indk; */ |
---|
520 | int indi, indj, index; |
---|
521 | int length; |
---|
522 | /* int find_pattern(), Lenstr(); */ |
---|
523 | /* int paren_string(), Skip_white_space(), Reach_white_space(); */ |
---|
524 | char buffer[LONGTEXT], temp[LONGTEXT], pstring[LONGTEXT]; |
---|
525 | char atcc[LONGTEXT]; |
---|
526 | /* char *Catstr(), *Dupstr(); */ |
---|
527 | /* void get_atcc_string(); */ |
---|
528 | |
---|
529 | atcc[0]='\0'; |
---|
530 | for(indi=0; indi<cc_num; indi++) { |
---|
531 | index=0; |
---|
532 | while((index=paren_string(source, pstring, index))>0) { |
---|
533 | if((indj=find_pattern(pstring, CC[indi]))>=0){ |
---|
534 | /* skip the key word */ |
---|
535 | indj += Lenstr(CC[indi]); |
---|
536 | /* skip blank spaces */ |
---|
537 | indj=Skip_white_space(pstring, indj); |
---|
538 | /* get strain */ |
---|
539 | get_atcc_string(pstring, buffer, indj); |
---|
540 | sprintf(temp, "%s %s", CC[indi], buffer); |
---|
541 | length=Lenstr(atcc); |
---|
542 | if(length>0) { |
---|
543 | atcc[length]= '\0'; |
---|
544 | Catstr(atcc, ", "); |
---|
545 | } |
---|
546 | Catstr(atcc, temp); |
---|
547 | } /* find atcc */ |
---|
548 | } /* while loop */ |
---|
549 | } /* for loop */ |
---|
550 | /* append eoln to the atcc string */ |
---|
551 | length = Lenstr(atcc); |
---|
552 | if (data.macke.atcc) { |
---|
553 | data.macke.atcc[length] = '\0'; |
---|
554 | } |
---|
555 | Catstr(atcc, "\n"); |
---|
556 | return(Dupstr(atcc)); |
---|
557 | } |
---|
558 | /* ----------------------------------------------------------------- */ |
---|
559 | /* Function paren_string() |
---|
560 | */ |
---|
561 | int |
---|
562 | paren_string(string, pstring, index) |
---|
563 | char *string, *pstring; |
---|
564 | int index; |
---|
565 | { |
---|
566 | int pcount=0, len, indi; |
---|
567 | |
---|
568 | for(indi=0, len=Lenstr(string); index<len; index++) { |
---|
569 | if(pcount>=1) pstring[indi++]=string[index]; |
---|
570 | if(string[index]=='(') pcount++; |
---|
571 | if(string[index]==')') pcount--; |
---|
572 | } |
---|
573 | if(indi==0) return(-1); |
---|
574 | pstring[--indi]='\0'; |
---|
575 | return(index); |
---|
576 | } |
---|
577 | /* ---------------------------------------------------------------- |
---|
578 | * Function num_of_remark(). |
---|
579 | * Count num of remarks needed in order to alloc spaces. |
---|
580 | */ |
---|
581 | int |
---|
582 | num_of_remark() { |
---|
583 | |
---|
584 | int remnum, /*indi, */indj, length; |
---|
585 | |
---|
586 | remnum = 0; |
---|
587 | /* count references to be put into remarks */ |
---|
588 | if(data.gbk.numofref>0&&Lenstr(data.gbk.reference[0].ref)>1) |
---|
589 | remnum++; |
---|
590 | for(indj=1; indj<data.gbk.numofref; indj++) { |
---|
591 | if(Lenstr(data.gbk.reference[indj].ref)>1) |
---|
592 | remnum++; |
---|
593 | if(Lenstr(data.gbk.reference[indj].journal)>1) |
---|
594 | remnum++; |
---|
595 | if(Lenstr(data.gbk.reference[indj].author)>1) |
---|
596 | remnum++; |
---|
597 | if(Lenstr(data.gbk.reference[indj].title)>1) |
---|
598 | remnum++; |
---|
599 | if(Lenstr(data.gbk.reference[indj].standard)>1) |
---|
600 | remnum++; |
---|
601 | } /* loop for copying other reference */ |
---|
602 | /* count the other keyword in GenBank format to be put into remarks */ |
---|
603 | if(Lenstr(data.gbk.keywords)>1) |
---|
604 | remnum++; |
---|
605 | if(Lenstr(data.gbk.accession)>1) |
---|
606 | remnum++; |
---|
607 | if(Lenstr(data.gbk.comments.orginf.source)>1) /* Source of strain */ |
---|
608 | remnum++; |
---|
609 | if(Lenstr(data.gbk.comments.orginf.formname)>1) |
---|
610 | remnum++; |
---|
611 | if(Lenstr(data.gbk.comments.orginf.nickname)>1) /* Alternate name */ |
---|
612 | remnum++; |
---|
613 | if(Lenstr(data.gbk.comments.orginf.commname)>1) |
---|
614 | remnum++; |
---|
615 | if(Lenstr(data.gbk.comments.orginf.hostorg)>1) /* host organism */ |
---|
616 | remnum++; |
---|
617 | if(Lenstr(data.gbk.comments.seqinf.RDPid)>1) |
---|
618 | remnum++; |
---|
619 | if(Lenstr(data.gbk.comments.seqinf.methods)>1) |
---|
620 | remnum++; |
---|
621 | if(data.gbk.comments.seqinf.comp3!=' ') |
---|
622 | remnum++; |
---|
623 | if(data.gbk.comments.seqinf.comp5!=' ') |
---|
624 | remnum++; |
---|
625 | /* counting other than specific keyword comments */ |
---|
626 | if(Lenstr(data.gbk.comments.others)>0) { |
---|
627 | length = Lenstr(data.gbk.comments.others); |
---|
628 | for(indj=0; indj<length; indj++) |
---|
629 | { |
---|
630 | if(data.gbk.comments.others[indj]=='\n' |
---|
631 | || data.gbk.comments.others[indj]=='\0') { |
---|
632 | remnum++; |
---|
633 | } /* new remark line */ |
---|
634 | } /* for loop to find other remarks */ |
---|
635 | } /* other comments */ |
---|
636 | return(remnum); |
---|
637 | } |
---|
638 | /* ----------------------------------------------------------------- |
---|
639 | * Function macke_to_genbank(). |
---|
640 | * Convert from macke format to genbank format. |
---|
641 | */ |
---|
642 | void |
---|
643 | macke_to_genbank(inf, outf) |
---|
644 | char *inf, *outf; |
---|
645 | { |
---|
646 | FILE *IFP1, *IFP2, *IFP3, *ofp; |
---|
647 | FILE_BUFFER ifp1, ifp2, ifp3; |
---|
648 | char temp[TOKENNUM]; |
---|
649 | |
---|
650 | if((IFP1=fopen(inf, "r"))==NULL|| |
---|
651 | (IFP2=fopen(inf, "r"))==NULL|| |
---|
652 | (IFP3=fopen(inf, "r"))==NULL) { |
---|
653 | sprintf(temp, "Cannot open input file %s\n", inf); |
---|
654 | error(19, temp); |
---|
655 | } |
---|
656 | |
---|
657 | ifp1 = create_FILE_BUFFER(inf, IFP1); |
---|
658 | ifp2 = create_FILE_BUFFER(inf, IFP2); |
---|
659 | ifp3 = create_FILE_BUFFER(inf, IFP3); |
---|
660 | |
---|
661 | if(Lenstr(outf)<=0) ofp = stdout; |
---|
662 | else if((ofp=fopen(outf, "w"))==NULL) { |
---|
663 | sprintf(temp, "Cannot open output file %s\n", outf); |
---|
664 | error(44, temp); |
---|
665 | } |
---|
666 | init(); |
---|
667 | init_seq_data(); |
---|
668 | init_gm_data(); |
---|
669 | |
---|
670 | #ifdef log |
---|
671 | fprintf(stderr, "Start converting...\n"); |
---|
672 | #endif |
---|
673 | |
---|
674 | while(macke_in(ifp1, ifp2, ifp3)!=EOF) { |
---|
675 | data.numofseq++; |
---|
676 | if(mtog()) genbank_out(ofp); |
---|
677 | else error(15, "Conversion from macke to genbank fails, Exit"); |
---|
678 | init_gm_data(); |
---|
679 | |
---|
680 | #ifdef log |
---|
681 | if((data.numofseq % 50)==0) |
---|
682 | fprintf(stderr, |
---|
683 | "%d sequences are converted...\n", |
---|
684 | data.numofseq); |
---|
685 | #endif |
---|
686 | |
---|
687 | } |
---|
688 | |
---|
689 | #ifdef log |
---|
690 | fprintf(stderr, |
---|
691 | "Total %d sequences have been processed\n", data.numofseq); |
---|
692 | #endif |
---|
693 | |
---|
694 | } |
---|
695 | /* ---------------------------------------------------------------- |
---|
696 | * Function mtog(). |
---|
697 | * Convert Macke format to Genbank format. |
---|
698 | */ |
---|
699 | int |
---|
700 | mtog() { |
---|
701 | int indi; |
---|
702 | /* int len, Lenstr(), Cmpstr(); */ |
---|
703 | char temp[LONGTEXT]; |
---|
704 | /* char *today_date(); */ |
---|
705 | /* char *Dupstr(), *Reallocspace(), *macke_copyrem(); */ |
---|
706 | /* char *genbank_date(); */ |
---|
707 | /* void Freespace(), Cpystr(), Append(), Append_char(); */ |
---|
708 | /* void mtog_genbank_def_and_source(); */ |
---|
709 | /* void mtog_decode_ref_and_remarks(); */ |
---|
710 | /* void init_reference(), replace_entry(), warning(); */ |
---|
711 | |
---|
712 | Cpystr(temp, data.macke.seqabbr); |
---|
713 | |
---|
714 | for(indi=Lenstr(temp); indi<13; temp[indi++] = ' ') ; |
---|
715 | |
---|
716 | if(Lenstr(data.macke.date)>1) |
---|
717 | |
---|
718 | sprintf((temp+10), |
---|
719 | "%7d bp RNA RNA %s\n", |
---|
720 | data.seq_length, genbank_date(data.macke.date)); |
---|
721 | |
---|
722 | else sprintf((temp+10), |
---|
723 | "%7d bp RNA RNA %s\n", |
---|
724 | data.seq_length, genbank_date(today_date())); |
---|
725 | |
---|
726 | replace_entry(&(data.gbk.locus), temp); |
---|
727 | |
---|
728 | /* GenBank ORGANISM */ |
---|
729 | if(Lenstr(data.macke.name)>1) { |
---|
730 | replace_entry(&(data.gbk.organism), data.macke.name); |
---|
731 | |
---|
732 | /* append a '.' at the end */ |
---|
733 | Append_char(&(data.gbk.organism), '.'); |
---|
734 | } |
---|
735 | |
---|
736 | if(Lenstr(data.macke.rna)>1) { |
---|
737 | data.gbk.comments.seqinf.exist = 1; |
---|
738 | replace_entry(&(data.gbk.comments.seqinf.methods), |
---|
739 | data.macke.rna); |
---|
740 | } |
---|
741 | if(Lenstr(data.macke.acs)>1) { |
---|
742 | /* #### not converted to accession but to comment gbkentry only, temporarily |
---|
743 | Freespace(&(data.gbk.accession)); |
---|
744 | data.gbk.accession = Dupstr(data.macke.acs); |
---|
745 | */ |
---|
746 | data.gbk.comments.seqinf.exist = 1; |
---|
747 | replace_entry(&(data.gbk.comments.seqinf.gbkentry), |
---|
748 | data.macke.acs); |
---|
749 | } else if(Lenstr(data.macke.nbk)>1) { |
---|
750 | /* #### not converted to accession but to comment gbkentry only, temp |
---|
751 | Freespace(&(data.gbk.accession)); |
---|
752 | data.gbk.accession = Dupstr(data.macke.nbk); |
---|
753 | */ |
---|
754 | data.gbk.comments.seqinf.exist = 1; |
---|
755 | replace_entry(&(data.gbk.comments.seqinf.gbkentry), |
---|
756 | data.macke.nbk); |
---|
757 | } |
---|
758 | if(Lenstr(data.macke.atcc)>1) { |
---|
759 | data.gbk.comments.orginf.exist = 1; |
---|
760 | replace_entry(&(data.gbk.comments.orginf.cc), |
---|
761 | data.macke.atcc); |
---|
762 | } |
---|
763 | mtog_decode_ref_and_remarks(); |
---|
764 | /* final conversion of cc */ |
---|
765 | if(Lenstr(data.gbk.comments.orginf.cc)<=1&&Lenstr(data.macke.atcc)>1){ |
---|
766 | replace_entry(&(data.gbk.comments.orginf.cc), |
---|
767 | data.macke.atcc); |
---|
768 | } |
---|
769 | |
---|
770 | /* define GenBank DEFINITION, after GenBank KEYWORD is defined. */ |
---|
771 | mtog_genbank_def_and_source(); |
---|
772 | |
---|
773 | return(1); |
---|
774 | } |
---|
775 | /* --------------------------------------------------------------- |
---|
776 | * Function mtog_decode_remarks(). |
---|
777 | * Decode remarks of Macke to GenBank format. |
---|
778 | */ |
---|
779 | void |
---|
780 | mtog_decode_ref_and_remarks() { |
---|
781 | |
---|
782 | int indi, indj; |
---|
783 | int acount, tcount, jcount, rcount, scount; |
---|
784 | char key[TOKENNUM], temp[LONGTEXT]; |
---|
785 | /* char *macke_copyrem(), *Reallocspace(), *Dupstr(); */ |
---|
786 | /* void Append_char(), Append(), Cpystr(); */ |
---|
787 | /* void mtog_copy_remark(), init_reference(); */ |
---|
788 | |
---|
789 | data.gbk.numofref=acount=tcount=jcount=rcount=scount=0; |
---|
790 | |
---|
791 | if(Lenstr(data.macke.author)>1) { |
---|
792 | if((acount+1)>data.gbk.numofref) { |
---|
793 | /* new reference */ |
---|
794 | data.gbk.reference = (Reference*)Reallocspace(data.gbk.reference, sizeof(Reference)*(acount+1)); |
---|
795 | data.gbk.numofref = acount+1; |
---|
796 | init_reference(&(data.gbk.reference[acount]), AUTHOR); |
---|
797 | } else acount = data.gbk.numofref - 1; |
---|
798 | data.gbk.reference[acount++].author |
---|
799 | = (char*)Dupstr(data.macke.author); |
---|
800 | } |
---|
801 | if(Lenstr(data.macke.journal)>1) { |
---|
802 | if((jcount+1)>data.gbk.numofref) { |
---|
803 | data.gbk.reference = |
---|
804 | (Reference*)Reallocspace(data.gbk.reference, |
---|
805 | sizeof(Reference)*(jcount+1)); |
---|
806 | data.gbk.numofref = jcount+1; |
---|
807 | init_reference(&(data.gbk.reference[jcount]), JOURNAL); |
---|
808 | } else jcount = data.gbk.numofref - 1; |
---|
809 | data.gbk.reference[jcount++].journal |
---|
810 | = (char*)Dupstr(data.macke.journal); |
---|
811 | } |
---|
812 | if(Lenstr(data.macke.title)>1) { |
---|
813 | if((tcount+1)>data.gbk.numofref) { |
---|
814 | data.gbk.reference = |
---|
815 | (Reference*)Reallocspace(data.gbk.reference, |
---|
816 | sizeof(Reference)*(tcount+1)); |
---|
817 | data.gbk.numofref = tcount+1; |
---|
818 | init_reference(&(data.gbk.reference[tcount]), TITLE); |
---|
819 | } else tcount = data.gbk.numofref - 1; |
---|
820 | data.gbk.reference[tcount++].title |
---|
821 | = (char*)Dupstr(data.macke.title); |
---|
822 | } |
---|
823 | for(indi=0; indi<data.macke.numofrem; indi++) { |
---|
824 | indj = macke_key_word(data.macke.remarks[indi], |
---|
825 | 0, key, TOKENNUM); |
---|
826 | if(Cmpstr(key, "KEYWORDS")==EQ) { |
---|
827 | mtog_copy_remark(&(data.gbk.keywords), |
---|
828 | &indi, indj); |
---|
829 | |
---|
830 | /* append a '.' at the end */ |
---|
831 | Append_char(&(data.gbk.keywords), '.'); |
---|
832 | |
---|
833 | } else if(Cmpstr(key, "GenBank ACCESSION")==EQ) { |
---|
834 | mtog_copy_remark(&(data.gbk.accession), |
---|
835 | &indi, indj); |
---|
836 | |
---|
837 | } else if(Cmpstr(key, "ref")==EQ) { |
---|
838 | if((rcount+1)>data.gbk.numofref) { |
---|
839 | /* new reference */ |
---|
840 | data.gbk.reference = (Reference*) |
---|
841 | Reallocspace(data.gbk.reference, |
---|
842 | sizeof(Reference)*(rcount+1)); |
---|
843 | data.gbk.numofref = rcount+1; |
---|
844 | init_reference(&(data.gbk.reference[rcount]), |
---|
845 | REF); |
---|
846 | } else rcount = data.gbk.numofref - 1; |
---|
847 | data.gbk.reference[rcount++].ref |
---|
848 | = macke_copyrem(data.macke.remarks, &indi, |
---|
849 | data.macke.numofrem, indj); |
---|
850 | } else if(Cmpstr(key, "auth")==EQ) { |
---|
851 | if((acount+1)>data.gbk.numofref) { |
---|
852 | /* new reference */ |
---|
853 | data.gbk.reference = (Reference*) |
---|
854 | Reallocspace(data.gbk.reference, |
---|
855 | sizeof(Reference)*(acount+1)); |
---|
856 | data.gbk.numofref = acount+1; |
---|
857 | init_reference(&(data.gbk.reference[acount]), |
---|
858 | AUTHOR); |
---|
859 | } else acount = data.gbk.numofref - 1; |
---|
860 | data.gbk.reference[acount++].author |
---|
861 | = macke_copyrem(data.macke.remarks, &indi, |
---|
862 | data.macke.numofrem, indj); |
---|
863 | } else if(Cmpstr(key, "title")==EQ) { |
---|
864 | if((tcount+1)>data.gbk.numofref) { |
---|
865 | data.gbk.reference = (Reference*) |
---|
866 | Reallocspace(data.gbk.reference, |
---|
867 | sizeof(Reference)*(tcount+1)); |
---|
868 | data.gbk.numofref = tcount+1; |
---|
869 | init_reference(&(data.gbk.reference[tcount]), |
---|
870 | TITLE); |
---|
871 | } else tcount = data.gbk.numofref - 1; |
---|
872 | data.gbk.reference[tcount++].title |
---|
873 | = macke_copyrem(data.macke.remarks, &indi, |
---|
874 | data.macke.numofrem, indj); |
---|
875 | } else if(Cmpstr(key, "jour")==EQ) { |
---|
876 | if((jcount+1)>data.gbk.numofref) { |
---|
877 | data.gbk.reference = (Reference*) |
---|
878 | Reallocspace(data.gbk.reference, |
---|
879 | sizeof(Reference)*(jcount+1)); |
---|
880 | data.gbk.numofref = jcount+1; |
---|
881 | init_reference(&(data.gbk.reference[jcount]), |
---|
882 | JOURNAL); |
---|
883 | } else jcount = data.gbk.numofref - 1; |
---|
884 | data.gbk.reference[jcount++].journal |
---|
885 | = macke_copyrem(data.macke.remarks, &indi, |
---|
886 | data.macke.numofrem, indj); |
---|
887 | } else if(Cmpstr(key, "standard")==EQ) { |
---|
888 | if((scount+1)>data.gbk.numofref) { |
---|
889 | data.gbk.reference = (Reference*) |
---|
890 | Reallocspace(data.gbk.reference, |
---|
891 | sizeof(Reference)*(scount+1)); |
---|
892 | data.gbk.numofref = scount+1; |
---|
893 | init_reference(&(data.gbk.reference[scount]), |
---|
894 | STANDARD); |
---|
895 | } else scount = data.gbk.numofref - 1; |
---|
896 | data.gbk.reference[scount++].standard |
---|
897 | = macke_copyrem(data.macke.remarks, &indi, |
---|
898 | data.macke.numofrem, indj); |
---|
899 | |
---|
900 | } else if(Cmpstr(key, "Source of strain")==EQ) { |
---|
901 | |
---|
902 | data.gbk.comments.orginf.exist = 1; |
---|
903 | mtog_copy_remark( |
---|
904 | &(data.gbk.comments.orginf.source), |
---|
905 | &indi, indj); |
---|
906 | |
---|
907 | } else if(Cmpstr(key, "Former name")==EQ) { |
---|
908 | |
---|
909 | data.gbk.comments.orginf.exist = 1; |
---|
910 | mtog_copy_remark( |
---|
911 | &(data.gbk.comments.orginf.formname), |
---|
912 | &indi, indj); |
---|
913 | |
---|
914 | } else if(Cmpstr(key, "Alternate name")==EQ) { |
---|
915 | |
---|
916 | data.gbk.comments.orginf.exist = 1; |
---|
917 | mtog_copy_remark( |
---|
918 | &(data.gbk.comments.orginf.nickname), |
---|
919 | &indi, indj); |
---|
920 | |
---|
921 | } else if(Cmpstr(key, "Common name")==EQ) { |
---|
922 | |
---|
923 | data.gbk.comments.orginf.exist = 1; |
---|
924 | mtog_copy_remark( |
---|
925 | &(data.gbk.comments.orginf.commname), |
---|
926 | &indi, indj); |
---|
927 | |
---|
928 | } else if(Cmpstr(key, "Host organism")==EQ) { |
---|
929 | |
---|
930 | data.gbk.comments.orginf.exist = 1; |
---|
931 | mtog_copy_remark( |
---|
932 | &(data.gbk.comments.orginf.hostorg), |
---|
933 | &indi, indj); |
---|
934 | |
---|
935 | } else if(Cmpstr(key, "RDP ID")==EQ) { |
---|
936 | |
---|
937 | data.gbk.comments.seqinf.exist = 1; |
---|
938 | mtog_copy_remark( |
---|
939 | &(data.gbk.comments.seqinf.RDPid), |
---|
940 | &indi, indj); |
---|
941 | |
---|
942 | } else if(Cmpstr(key, "Sequencing methods")==EQ) { |
---|
943 | |
---|
944 | data.gbk.comments.seqinf.exist = 1; |
---|
945 | mtog_copy_remark( |
---|
946 | &(data.gbk.comments.seqinf.methods), |
---|
947 | &indi, indj); |
---|
948 | |
---|
949 | } else if(Cmpstr(key, "3' end complete")==EQ) { |
---|
950 | |
---|
951 | data.gbk.comments.seqinf.exist = 1; |
---|
952 | sscanf(data.macke.remarks[indi]+indj, "%s", key); |
---|
953 | if(Cmpstr(key, "Yes")==EQ) |
---|
954 | data.gbk.comments.seqinf.comp3 = 'y'; |
---|
955 | else data.gbk.comments.seqinf.comp3 = 'n'; |
---|
956 | |
---|
957 | } else if(Cmpstr(key, "5' end complete")==EQ) { |
---|
958 | |
---|
959 | data.gbk.comments.seqinf.exist = 1; |
---|
960 | sscanf(data.macke.remarks[indi]+indj, "%s", key); |
---|
961 | |
---|
962 | if(Cmpstr(key, "Yes")==EQ) |
---|
963 | data.gbk.comments.seqinf.comp5 |
---|
964 | = 'y'; |
---|
965 | else data.gbk.comments.seqinf.comp5 |
---|
966 | = 'n'; |
---|
967 | |
---|
968 | } else { /* other comments */ |
---|
969 | Cpystr(temp, data.macke.remarks[indi]); |
---|
970 | if(data.gbk.comments.others==NULL) |
---|
971 | data.gbk.comments.others |
---|
972 | = (char*)Dupstr(temp); |
---|
973 | else Append(&(data.gbk.comments.others), temp); |
---|
974 | } |
---|
975 | } /* for each rem */ |
---|
976 | } |
---|
977 | /* --------------------------------------------------------------- |
---|
978 | * Function mtog_copy_remark(). |
---|
979 | * Convert one remark back to GenBank format. |
---|
980 | */ |
---|
981 | void |
---|
982 | mtog_copy_remark(string, indi, indj) |
---|
983 | char **string; |
---|
984 | int *indi, indj; |
---|
985 | { |
---|
986 | /* void Freespace(); */ |
---|
987 | /* char *macke_copyrem(); */ |
---|
988 | |
---|
989 | Freespace(string); |
---|
990 | (*string) = (char*)macke_copyrem(data.macke.remarks, indi, |
---|
991 | data.macke.numofrem, indj); |
---|
992 | } |
---|
993 | /* ------------------------------------------------------------------ |
---|
994 | * Function macke_copyrem(). |
---|
995 | * uncode rem lines. |
---|
996 | */ |
---|
997 | char *macke_copyrem(strings, index, maxline, pointer) |
---|
998 | char **strings; |
---|
999 | int *index, maxline, pointer; |
---|
1000 | { |
---|
1001 | char *string; |
---|
1002 | int indi; |
---|
1003 | /* int len, length, macke_rem_continue_line(); */ |
---|
1004 | /* char *Catstr(), *Dupstr(); */ |
---|
1005 | /* void Append_rp_eoln(); */ |
---|
1006 | |
---|
1007 | string = (char*)Dupstr(strings[(*index)]+pointer); |
---|
1008 | for(indi=(*index)+1; indi<maxline |
---|
1009 | &&macke_rem_continue_line(strings, indi); indi++) |
---|
1010 | Append_rp_eoln(&string, strings[indi]+3); |
---|
1011 | (*index) = indi-1; |
---|
1012 | return(string); |
---|
1013 | } |
---|
1014 | /* ------------------------------------------------------------------ |
---|
1015 | * Function mtog_genbank_def_and_source(). |
---|
1016 | * Define GenBank DEFINITION and SOURCE lines the way RDP |
---|
1017 | * group likes. |
---|
1018 | */ |
---|
1019 | void |
---|
1020 | mtog_genbank_def_and_source() { |
---|
1021 | |
---|
1022 | /* int Lenstr(); */ |
---|
1023 | /* void Freespace(), Append(), Append_rm_eoln(), Append_char(); */ |
---|
1024 | /* void replace_entry(), warning(); */ |
---|
1025 | |
---|
1026 | if(Lenstr(data.macke.name)>1) |
---|
1027 | replace_entry(&(data.gbk.definition), |
---|
1028 | data.macke.name); |
---|
1029 | |
---|
1030 | if(Lenstr(data.macke.subspecies)>1) { |
---|
1031 | |
---|
1032 | if(Lenstr(data.gbk.definition)<=1) { |
---|
1033 | warning(22, "Genus and Species not defined"); |
---|
1034 | Append_rm_eoln(&(data.gbk.definition), "subsp. "); |
---|
1035 | } else Append_rm_eoln(&(data.gbk.definition), " subsp. "); |
---|
1036 | |
---|
1037 | Append(&(data.gbk.definition), data.macke.subspecies); |
---|
1038 | } |
---|
1039 | |
---|
1040 | if(Lenstr(data.macke.strain)>1) { |
---|
1041 | |
---|
1042 | if(Lenstr(data.gbk.definition)<=1) { |
---|
1043 | warning(23, |
---|
1044 | "Genus and Species and Subspecies not defined"); |
---|
1045 | Append_rm_eoln(&(data.gbk.definition), "str. "); |
---|
1046 | } else Append_rm_eoln(&(data.gbk.definition), " str. "); |
---|
1047 | |
---|
1048 | Append(&(data.gbk.definition), data.macke.strain); |
---|
1049 | } |
---|
1050 | |
---|
1051 | /* create SOURCE line, temp. */ |
---|
1052 | if(Lenstr(data.gbk.definition)>1) { |
---|
1053 | replace_entry(&(data.gbk.source), data.gbk.definition); |
---|
1054 | Append_char(&(data.gbk.source), '.'); |
---|
1055 | } |
---|
1056 | |
---|
1057 | /* append keyword to definition, if there is keyword. */ |
---|
1058 | if(Lenstr(data.gbk.keywords)>1) { |
---|
1059 | |
---|
1060 | if(Lenstr(data.gbk.definition)>1) |
---|
1061 | Append_rm_eoln(&(data.gbk.definition), |
---|
1062 | "; \n"); |
---|
1063 | |
---|
1064 | /* Here keywords must be ended by a '.' already */ |
---|
1065 | Append_rm_eoln(&(data.gbk.definition), |
---|
1066 | data.gbk.keywords); |
---|
1067 | |
---|
1068 | } else Append_rm_eoln((&data.gbk.definition), ".\n"); |
---|
1069 | |
---|
1070 | } |
---|
1071 | /* ------------------------------------------------------------------- |
---|
1072 | * Function get_string(). |
---|
1073 | * Get the rest of the string untill reaching certain |
---|
1074 | * terminators, such as ';', ',', '.',... |
---|
1075 | * Always append "\n" at the end of the returned string. |
---|
1076 | */ |
---|
1077 | void |
---|
1078 | get_string(line, temp, index) |
---|
1079 | char *line, *temp; |
---|
1080 | int index; |
---|
1081 | { |
---|
1082 | int indk, len, paren_num; |
---|
1083 | /* int not_ending_mark(); */ |
---|
1084 | |
---|
1085 | len = Lenstr(line); |
---|
1086 | paren_num=0; |
---|
1087 | for(indk=0; index<len; index++, indk++) { |
---|
1088 | temp[indk]=line[index]; |
---|
1089 | if(temp[indk]=='(') paren_num++; |
---|
1090 | if(temp[indk]==')') |
---|
1091 | if(paren_num==0) break; |
---|
1092 | else paren_num--; |
---|
1093 | else if(temp[indk]=='\n'||(paren_num==0 |
---|
1094 | &&temp[indk]==';')) break; |
---|
1095 | } |
---|
1096 | if(indk>1 && !(not_ending_mark(temp[indk-1]))) indk--; |
---|
1097 | temp[indk++]='\n'; |
---|
1098 | temp[indk]='\0'; |
---|
1099 | } |
---|
1100 | /* ------------------------------------------------------------------- |
---|
1101 | * Function get_atcc_string(). |
---|
1102 | * Get the rest of the string untill reaching certain |
---|
1103 | * terminators, such as ';', ',', '.',... |
---|
1104 | */ |
---|
1105 | void |
---|
1106 | get_atcc_string(line, temp, index) |
---|
1107 | char *line, *temp; |
---|
1108 | int index; |
---|
1109 | { |
---|
1110 | int indk, len, paren_num; |
---|
1111 | |
---|
1112 | len = Lenstr(line); |
---|
1113 | paren_num=0; |
---|
1114 | for(indk=0; index<len; index++, indk++){ |
---|
1115 | temp[indk]=line[index]; |
---|
1116 | if(temp[indk]=='(') paren_num++; |
---|
1117 | if(temp[indk]==')') |
---|
1118 | if(paren_num==0) break; |
---|
1119 | else paren_num--; |
---|
1120 | else if(paren_num==0&&(temp[indk]==';'||temp[indk]=='.' |
---|
1121 | ||temp[indk]==','||temp[indk]=='/'||temp[indk]=='\n')) |
---|
1122 | break; |
---|
1123 | } |
---|
1124 | temp[indk]='\0'; |
---|
1125 | } |
---|