1 | /********* Sequence input routines for CLUSTALV *******************/ |
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2 | #include <stdio.h> |
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3 | #include <string.h> |
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4 | #include <ctype.h> |
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5 | #include <stdlib.h> |
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6 | #include "clustalv.h" |
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7 | |
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8 | |
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9 | /* |
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10 | * Prototypes |
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11 | */ |
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12 | |
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13 | extern Boolean linetype(const char *,const char *); |
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14 | extern void warning(const char *,...); |
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15 | extern void error(const char *,...); |
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16 | extern char * rtrim(char *); |
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17 | extern void getstr(const char *,char *, int); |
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18 | |
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19 | void fill_chartab(void); |
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20 | int readseqs(int); |
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21 | |
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22 | static void get_seq(char *,char *,int *,char *); |
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23 | static void check_infile(int *); |
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24 | static void p_encode(char *, char *, int); |
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25 | static void n_encode(char *, char *, int); |
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26 | static int res_index(const char *,char); |
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27 | static Boolean check_dnaflag(char *, int); |
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28 | /* |
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29 | * Global variables |
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30 | */ |
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31 | |
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32 | extern FILE *fin; |
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33 | extern Boolean usemenu, dnaflag, explicit_dnaflag; |
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34 | extern char seqname[]; |
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35 | extern int nseqs; |
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36 | extern int *seqlen_array; |
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37 | extern char **names,**titles; |
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38 | extern char **seq_array; |
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39 | extern int profile1_empty, profile2_empty; |
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40 | |
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41 | const char *amino_acid_codes = "ABCDEFGHIKLMNPQRSTUVWXYZ-"; |
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42 | const char *amino_acid_order = "XCSTPAGNDEQHRKMILVFYW"; |
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43 | const char *nucleic_acid_order = "NACGTU"; |
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44 | static int seqFormat; |
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45 | static char chartab[256]; |
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46 | static const char *formatNames[] = {"unknown","EMBL/Swiss-Prot","PIR","Pearson"}; |
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47 | |
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48 | void fill_chartab() /* Create translation and check table */ |
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49 | { |
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50 | /* static char valid[]="ABCDEFGHIKLMNPQRSTVWXYZ-"; */ |
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51 | register int i; |
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52 | register char c; |
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53 | |
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54 | for(i=0;i<256;chartab[i++]=0); |
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55 | for(i=0;c=amino_acid_codes[i];i++) |
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56 | chartab[c]=chartab[tolower(c)]=c; |
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57 | } |
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58 | |
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59 | |
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60 | |
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61 | static void get_seq(char *sname,char *seq,int *len,char *tit) |
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62 | { |
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63 | static char line[MAXLINE+1]; |
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64 | int i; |
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65 | unsigned char c; |
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66 | |
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67 | switch(seqFormat) { |
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68 | case EMBLSWISS: |
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69 | while( !linetype(line,"ID") ) |
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70 | fgets(line,MAXLINE+1,fin); |
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71 | |
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72 | strncpy(sname,line+5,MAXNAMES); /* remember entryname */ |
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73 | sname[MAXNAMES]=EOS; |
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74 | rtrim(sname); |
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75 | |
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76 | /* while( !linetype(line,"DE") ) |
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77 | fgets(line,MAXLINE+1,fin); |
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78 | strncpy(tit,line+5,MAXTITLES); |
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79 | tit[MAXTITLES]=EOS; |
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80 | i=strlen(tit); |
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81 | if(tit[i-1]=='\n') tit[i-1]=EOS; |
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82 | */ |
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83 | while( !linetype(line,"SQ") ) |
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84 | fgets(line,MAXLINE+1,fin); |
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85 | |
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86 | *len=0; |
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87 | while(fgets(line,MAXLINE+1,fin)) { |
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88 | for(i=0;*len < MAXLEN;i++) { |
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89 | c=line[i]; |
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90 | if(c == '\n' || c == EOS || c == '/') |
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91 | break; /* EOL */ |
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92 | |
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93 | if( (c=chartab[c])) |
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94 | seq[++(*len)]=c; |
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95 | } |
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96 | if(*len == MAXLEN || c == '/') break; |
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97 | } |
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98 | break; |
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99 | |
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100 | case PIR: |
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101 | while(*line != '>') |
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102 | fgets(line,MAXLINE+1,fin); |
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103 | |
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104 | strncpy(sname,line+4,MAXNAMES); |
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105 | sname[MAXNAMES]=EOS; |
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106 | for(i=MAXNAMES-1;i > 0;i--) |
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107 | if(isspace(sname[i])) { |
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108 | sname[i]=EOS; |
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109 | break; |
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110 | } |
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111 | |
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112 | fgets(line,MAXLINE+1,fin); |
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113 | strncpy(tit,line,MAXTITLES); |
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114 | tit[MAXTITLES]=EOS; |
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115 | i=strlen(tit); |
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116 | if(tit[i-1]=='\n') tit[i-1]=EOS; |
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117 | |
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118 | *len=0; |
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119 | while(fgets(line,MAXLINE+1,fin)) { |
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120 | for(i=0;*len < MAXLEN;i++) { |
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121 | c=line[i]; |
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122 | if(c == '\n' || c == EOS || c == '*') |
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123 | break; /* EOL */ |
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124 | |
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125 | if( (c=chartab[c])) |
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126 | seq[++(*len)]=c; |
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127 | } |
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128 | if(*len == MAXLEN || c == '*') break; |
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129 | } |
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130 | break; |
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131 | |
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132 | case PEARSON: |
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133 | while(*line != '>') |
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134 | fgets(line,MAXLINE+1,fin); |
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135 | |
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136 | strncpy(sname,line+1,MAXNAMES); |
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137 | sname[MAXNAMES]=EOS; |
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138 | for(i=MAXNAMES-1;i > 0;i--) |
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139 | if(isspace(sname[i])) { |
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140 | sname[i]=EOS; |
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141 | break; |
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142 | } |
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143 | *tit=EOS; |
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144 | |
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145 | *len=0; |
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146 | while(fgets(line,MAXLINE+1,fin)) { |
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147 | for(i=0;*len < MAXLEN;i++) { |
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148 | c=line[i]; |
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149 | if(c == '\n' || c == EOS || c == '>') |
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150 | break; /* EOL */ |
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151 | |
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152 | if( (c=chartab[c])) |
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153 | seq[++(*len)]=c; |
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154 | } |
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155 | if(*len == MAXLEN || c == '>') break; |
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156 | } |
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157 | break; |
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158 | } |
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159 | |
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160 | if(*len == MAXLEN) |
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161 | warning("Sequence %s truncated to %d residues", |
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162 | sname,MAXLEN); |
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163 | |
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164 | seq[*len+1]=EOS; |
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165 | } |
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166 | |
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167 | |
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168 | int readseqs(int first_seq) /*first_seq is the #no. of the first seq. to read */ |
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169 | { |
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170 | char line[FILENAMELEN+1]; |
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171 | static char seq1[MAXLEN+2],sname1[MAXNAMES+1],title[MAXTITLES+1]; |
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172 | int i,no_seqs; |
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173 | static int l1; |
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174 | static Boolean dnaflag1; |
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175 | |
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176 | if(usemenu) |
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177 | getstr("Enter the name of the sequence file",line, FILENAMELEN+1); |
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178 | else |
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179 | strcpy(line,seqname); |
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180 | if(*line == EOS) return -1; |
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181 | |
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182 | if((fin=fopen(line,"r"))==NULL) { |
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183 | error("Could not open sequence file %s",line); |
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184 | return -1; /* DES -1 => file not found */ |
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185 | } |
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186 | strcpy(seqname,line); |
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187 | no_seqs=0; |
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188 | check_infile(&no_seqs); |
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189 | printf("\nSequence format is %s\n",formatNames[seqFormat]); |
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190 | if(no_seqs == 0) |
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191 | return 0; /* return the number of seqs. (zero here)*/ |
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192 | |
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193 | if((no_seqs + first_seq -1) > MAXN) { |
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194 | error("Too many sequences. Maximum is %d",MAXN); |
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195 | return 0; /* also return zero if too many */ |
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196 | } |
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197 | |
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198 | for(i=first_seq;i<=first_seq+no_seqs-1;++i) { /* get the seqs now*/ |
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199 | get_seq(sname1,seq1,&l1,title); |
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200 | seqlen_array[i]=l1; /* store the length */ |
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201 | strcpy(names[i],sname1); /* " " name */ |
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202 | strcpy(titles[i],title); /* " " title */ |
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203 | |
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204 | if(!explicit_dnaflag) { |
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205 | dnaflag1 = check_dnaflag(seq1,l1); /* check DNA/Prot */ |
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206 | if(i == 1) dnaflag = dnaflag1; |
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207 | } /* type decided by first seq*/ |
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208 | else |
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209 | dnaflag1 = dnaflag; |
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210 | |
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211 | if( (!explicit_dnaflag) && (dnaflag1 != dnaflag) ) |
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212 | warning( |
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213 | "Sequence %d [%s] appears to be of different type to sequence 1", |
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214 | i,sname1); |
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215 | |
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216 | if(dnaflag) |
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217 | n_encode(seq1,seq_array[i],l1); /* encode the sequence*/ |
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218 | else /* as ints */ |
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219 | p_encode(seq1,seq_array[i],l1); |
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220 | } |
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221 | |
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222 | fclose(fin); |
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223 | return no_seqs; /* return the number of seqs. read in this call */ |
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224 | } |
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225 | |
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226 | |
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227 | static Boolean check_dnaflag(char *seq, int slen) |
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228 | /* check if DNA or Protein |
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229 | The decision is based on counting all A,C,G,T,U or N. |
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230 | If >= 85% of all characters (except -) are as above => DNA */ |
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231 | { |
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232 | int i, c, nresidues, nbases; |
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233 | float ratio; |
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234 | |
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235 | nresidues = nbases = 0; |
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236 | for(i=1; i <= slen; i++) { |
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237 | if(seq[i] != '-') { |
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238 | nresidues++; |
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239 | if(seq[i] == 'N') |
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240 | nbases++; |
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241 | else { |
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242 | c = res_index(nucleic_acid_order, seq[i]); |
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243 | if(c > 0) |
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244 | nbases++; |
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245 | } |
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246 | } |
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247 | } |
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248 | if( (nbases == 0) || (nresidues == 0) ) return FALSE; |
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249 | ratio = (float)nbases/(float)nresidues; |
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250 | /* |
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251 | fprintf(stdout,"\n nbases = %d, nresidues = %d, ratio = %f\n", |
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252 | nbases,nresidues,ratio); |
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253 | */ |
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254 | if(ratio >= 0.85) |
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255 | return TRUE; |
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256 | else |
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257 | return FALSE; |
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258 | } |
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259 | |
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260 | |
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261 | |
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262 | static void check_infile(int *local_nseqs) |
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263 | { |
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264 | char line[MAXLINE+1]; |
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265 | |
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266 | *local_nseqs=0; |
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267 | fgets(line,MAXLINE+1,fin); |
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268 | if( linetype(line,"ID") ) /* EMBL/Swiss-Prot format ? */ |
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269 | seqFormat=EMBLSWISS; |
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270 | else if(*line == '>') /* no */ |
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271 | seqFormat=(line[3] == ';')?PIR:PEARSON; /* distinguish PIR and Pearson */ |
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272 | else { |
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273 | seqFormat=UNKNOWN; |
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274 | return; |
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275 | } |
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276 | |
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277 | (*local_nseqs)++; |
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278 | |
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279 | while(fgets(line,MAXLINE+1,fin) != NULL) { |
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280 | switch(seqFormat) { |
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281 | case EMBLSWISS: |
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282 | if( linetype(line,"ID") ) |
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283 | (*local_nseqs)++; |
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284 | break; |
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285 | case PIR: |
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286 | case PEARSON: |
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287 | if( *line == '>' ) |
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288 | (*local_nseqs)++; |
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289 | break; |
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290 | default: |
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291 | break; |
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292 | } |
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293 | } |
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294 | fseek(fin,0,0); |
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295 | } |
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296 | |
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297 | static void p_encode(char *seq, char *naseq, int l) |
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298 | { /* code seq as ints .. use -2 for gap */ |
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299 | register int i; |
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300 | /* static char *aacids="CSTPAGNDEQHRKMILVFYW";*/ |
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301 | |
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302 | for(i=1;i<=l;i++) |
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303 | if(seq[i] == '-') |
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304 | naseq[i] = -2; |
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305 | else if(seq[i] == 'X') |
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306 | naseq[i] = 0; |
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307 | else |
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308 | naseq[i] = res_index(amino_acid_order,seq[i]); |
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309 | } |
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310 | |
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311 | static void n_encode(char *seq,char *naseq,int l) |
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312 | { /* code seq as ints .. use -2 for gap */ |
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313 | register int i,c; |
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314 | /* static char *nucs="ACGTU"; */ |
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315 | |
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316 | for(i=1;i<=l;i++) { |
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317 | if(seq[i] == '-') /* if a gap character -> code = -2 */ |
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318 | naseq[i] = -2; /* this is the code for a gap in */ |
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319 | else { /* the input files */ |
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320 | c=res_index(nucleic_acid_order,seq[i]); |
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321 | if (c == 5) c=4; |
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322 | naseq[i]=c; |
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323 | } |
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324 | } |
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325 | } |
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326 | |
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327 | static int res_index(const char *t,char c) |
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328 | { |
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329 | register int i; |
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330 | |
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331 | for(i=0;t[i] && t[i] != c;i++) |
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332 | ; |
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333 | if(t[i]) return(i); |
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334 | else return 0; |
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335 | } |
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