| 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(char *,char *); |
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| 14 | extern void warning(char *,...); |
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| 15 | extern void error(char *,...); |
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| 16 | extern char * rtrim(char *); |
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| 17 | extern void getstr(char *,char *); |
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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(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 profile1_empty, profile2_empty; |
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| 40 | |
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| 41 | char *amino_acid_codes = "ABCDEFGHIKLMNPQRSTUVWXYZ-"; |
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| 42 | char *amino_acid_order = "XCSTPAGNDEQHRKMILVFYW"; |
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| 43 | 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 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,j,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); |
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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 *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 | *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 | (*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 | (*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 | (*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(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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