388 lines
9.9 KiB
C
388 lines
9.9 KiB
C
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#include <stdio.h>
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#include <malloc.h>
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#include <strings.h>
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#include "global_defs.h"
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char vert_mito[512][4] =
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{
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"AAA","Lys", "AAC","Asn", "AAG","Lys", "AAT","Asn", "ACA","Thr",
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"ACC","Thr", "ACG","Thr", "ACT","Thr", "AGA","Ter", "AGC","Ser",
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"AGG","Ter", "AGT","Ser", "ATA","Met", "ATC","Ile", "ATG","Met",
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"ATT","Ile", "CAA","Gln", "CAC","His", "CAG","Gln", "CAT","His",
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"CCA","Pro", "CCC","Pro", "CCG","Pro", "CCT","Pro", "CGA","Arg",
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"CGC","Arg", "CGG","Arg", "CGT","Arg", "CTA","Leu", "CTC","Leu",
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"CTG","Leu", "CTT","Leu", "GAA","Glu", "GAC","Asp", "GAG","Glu",
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"GAT","Asp", "GCA","Ala", "GCC","Ala", "GCG","Ala", "GCT","Ala",
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"GGA","Gly", "GGC","Gly", "GGG","Gly", "GGT","Gly", "GTA","Val",
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"GTC","Val", "GTG","Val", "GTT","Val", "TAA","Ter", "TAC","Tyr",
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"TAG","Ter", "TAT","Tyr", "TCA","Ser", "TCC","Ser", "TCG","Ser",
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"TCT","Ser", "TGA","Trp", "TGC","Cys", "TGG","Trp", "TGT","Cys",
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"TTA","Leu", "TTC","Phe", "TTG","Leu", "TTT","Phe"
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},
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mycoplasma[512][4] =
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{
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"AAA","Lys", "AAC","Asn", "AAG","Lys", "AAT","Asn", "ACA","Thr",
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"ACC","Thr", "ACG","Thr", "ACT","Thr", "AGA","Arg", "AGC","Ser",
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"AGG","Arg", "AGT","Ser", "ATA","Ile", "ATC","Ile", "ATG","Met",
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"ATT","Ile", "CAA","Gln", "CAC","His", "CAG","Gln", "CAT","His",
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"CCA","Pro", "CCC","Pro", "CCG","Pro", "CCT","Pro", "CGA","Arg",
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"CGC","Arg", "CGG","Arg", "CGT","Arg", "CTA","Leu", "CTC","Leu",
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"CTG","Leu", "CTT","Leu", "GAA","Glu", "GAC","Asp", "GAG","Glu",
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"GAT","Asp", "GCA","Ala", "GCC","Ala", "GCG","Ala", "GCT","Ala",
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"GGA","Gly", "GGC","Gly", "GGG","Gly", "GGT","Gly", "GTA","Val",
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"GTC","Val", "GTG","Val", "GTT","Val", "TAA","Ter", "TAC","Tyr",
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"TAG","Ter", "TAT","Tyr", "TCA","Ser", "TCC","Ser", "TCG","Ser",
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"TCT","Ser", "TGA","Trp", "TGC","Cys", "TGG","Trp", "TGT","Cys",
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"TTA","Leu", "TTC","Phe", "TTG","Leu", "TTT","Phe" },
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universal[512][4] =
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{
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"AAA","Lys", "AAC","Asn", "AAG","Lys", "AAT","Asn", "ACA","Thr",
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"ACC","Thr", "ACG","Thr", "ACT","Thr", "AGA","Arg", "AGC","Ser",
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"AGG","Arg", "AGT","Ser", "ATA","Ile", "ATC","Ile", "ATG","Met",
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"ATT","Ile", "CAA","Gln", "CAC","His", "CAG","Gln", "CAT","His",
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"CCA","Pro", "CCC","Pro", "CCG","Pro", "CCT","Pro", "CGA","Arg",
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"CGC","Arg", "CGG","Arg", "CGT","Arg", "CTA","Leu", "CTC","Leu",
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"CTG","Leu", "CTT","Leu", "GAA","Glu", "GAC","Asp", "GAG","Glu",
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"GAT","Asp", "GCA","Ala", "GCC","Ala", "GCG","Ala", "GCT","Ala",
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"GGA","Gly", "GGC","Gly", "GGG","Gly", "GGT","Gly", "GTA","Val",
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"GTC","Val", "GTG","Val", "GTT","Val", "TAA","Ter", "TAC","Tyr",
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"TAG","Ter", "TAT","Tyr", "TCA","Ser", "TCC","Ser", "TCG","Ser",
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"TCT","Ser", "TGA","Ter", "TGC","Cys", "TGG","Trp", "TGT","Cys",
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"TTA","Leu", "TTC","Phe", "TTG","Leu", "TTT","Phe" },
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yeast[512][4] =
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{
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"AAA","Lys", "AAC","Asn", "AAG","Lys", "AAT","Asn", "ACA","Thr",
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"ACC","Thr", "ACG","Thr", "ACT","Thr", "AGA","Arg", "AGC","Ser",
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"AGG","Arg", "AGT","Ser", "ATA","Met", "ATC","Ile", "ATG","Met",
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"ATT","Ile", "CAA","Gln", "CAC","His", "CAG","Gln", "CAT","His",
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"CCA","Pro", "CCC","Pro", "CCG","Pro", "CCT","Pro", "CGA","Arg",
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"CGC","Arg", "CGG","Arg", "CGT","Arg", "CTA","Thr", "CTC","Thr",
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"CTG","Thr", "CTT","Thr", "GAA","Glu", "GAC","Asp", "GAG","Glu",
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"GAT","Asp", "GCA","Ala", "GCC","Ala", "GCG","Ala", "GCT","Ala",
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"GGA","Gly", "GGC","Gly", "GGG","Gly", "GGT","Gly", "GTA","Val",
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"GTC","Val", "GTG","Val", "GTT","Val", "TAA","Ter", "TAC","Tyr",
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"TAG","Ter", "TAT","Tyr", "TCA","Ser", "TCC","Ser", "TCG","Ser",
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"TCT","Ser", "TGA","Trp", "TGC","Cys", "TGG","Trp", "TGT","Cys",
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"TTA","Leu", "TTC","Phe", "TTG","Leu", "TTT","Phe"
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};
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char three_to_one[23][5] = {
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"AlaA", "ArgR", "AsnN", "AspD",
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"AsxB", "CysC", "GlnQ", "GluE",
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"GlxZ", "GlyG", "HisH", "IleI",
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"LeuL", "LysK", "MetM", "PheF",
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"ProP", "SerS", "ThrT", "TrpW",
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"TyrY", "ValV", "Ter*"
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};
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main(ac,av)
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int ac;
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char **av;
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{
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int Success = TRUE,cursize,tbl,i,j,k,maxsize = 10,frame=1,
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min_frame = 0,ltrs=0, sep=0, tmp_num_frame, print_comp=FALSE;
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Sequence temp,*seqs;
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FILE *file;
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char number[5],tr_tbl[512][4];
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extern char *Realloc();
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extern Translate_NA_AA();
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if(ac == 1)
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{
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fprintf(stderr,
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"Options:[-tbl codon_table] [-frame #] [-min_frame #] [-3] [-sep] GDEfile\n");
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fprintf(stderr," 1=universal 1=first frame Shortest AA Three letter don't seperate\n");
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fprintf(stderr," 2=mycoplasma 2=second frame sequence codes groups\n");
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fprintf(stderr," 3=yeast 3=third frame to translate\n");
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fprintf(stderr," 4=Vert. mito. 6=All six\n");
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exit(0);
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}
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for(j=1;j<ac-1;j++)
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{
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if(strcmp(av[j],"-tbl")==0)
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{
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sscanf(av[++j],"%d",&tbl);
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}
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if(strcmp(av[j],"-frame")==0)
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{
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sscanf(av[++j],"%d",&frame);
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}
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if(strcmp(av[j],"-min_frame")==0)
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{
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sscanf(av[++j],"%d",&min_frame);
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}
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if(strcmp(av[j],"-3")==0)
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{
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ltrs = 1;
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}
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if(strcmp(av[j],"-sep")==0)
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{
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sep = 1;
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}
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}
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file = fopen(av[ac-1],"r");
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if(file == NULL)
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exit(-1);
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seqs = (Sequence*)Calloc(maxsize,sizeof(Sequence));
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for(cursize = 0;Success == TRUE;cursize++)
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{
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Success = ReadRecord(file,&(seqs[cursize]));
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if(cursize == maxsize-1)
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{
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maxsize *= 2;
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seqs = (Sequence*)Realloc(seqs, maxsize*sizeof(Sequence));
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}
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if(Success==TRUE)
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{
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seqs[cursize].group_number = 99999;
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}
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}
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cursize--;
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tmp_num_frame = frame; /*added by jckelley, 7/2/92 */
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for(j=0;j<cursize;j++)
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{
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frame = tmp_num_frame; /*added by jckelley, 7/2/92 */
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if(frame == 6)
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for(i=0;i<2;i++)
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{
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for(k=0;k<3;k++)
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{
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SeqCopy(&(seqs[j]),&temp);
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if(i==0)
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sprintf(number,"_%d",k+1);
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else
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sprintf(number,"_comp%d",k+1);
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strncat(temp.name,number,32);
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switch (tbl)
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{
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case 3:
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Translate_NA_AA(&temp,yeast,k,min_frame,ltrs,sep);
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break;
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case 4:
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Translate_NA_AA(&temp,vert_mito,k,min_frame,ltrs,sep);
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break;
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case 2:
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Translate_NA_AA(&temp,mycoplasma,k,min_frame,ltrs,sep);
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break;
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case 1:
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default:
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Translate_NA_AA(&temp,universal,k,min_frame,ltrs,sep);
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break;
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}
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/* WriteRecord(stdout,&temp,NULL,0); */
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}
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SeqRev(&(seqs[j]),seqs[j].offset,seqs[j].seqlen+
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seqs[j].offset-1);
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SeqComp(&(seqs[j]));
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}
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else
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{
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frame = (frame-1)%3;
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SeqCopy(&(seqs[j]),&temp);
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sprintf(number,"_%d",frame+1);
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strncat(temp.name,number,32);
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switch(tbl)
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{
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case 3:
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Translate_NA_AA(&temp,yeast,frame,min_frame,ltrs,sep);
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break;
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case 4:
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Translate_NA_AA(&temp,vert_mito,frame,min_frame,ltrs,sep);
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break;
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case 2:
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Translate_NA_AA(&temp,mycoplasma,frame,min_frame,ltrs,sep);
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break;
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case 1:
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default:
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Translate_NA_AA(&temp,universal,frame,min_frame,ltrs,sep);
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break;
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}
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}
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}
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exit(0);
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}
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Translate_NA_AA(seq,table,r_frame,min_frame,letter_code,sep)
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Sequence *seq;
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char table[][4];
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int r_frame,min_frame,letter_code, sep;
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{
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extern char *Realloc(), ThreeToOne();
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int i,true_start,k,pos,fptr = 0,start = 0;
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int last_start = 0,codon_count = 0;
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char c,codon[4],*temp, *save_c_elem, *save_name, strtmp[80];
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extern int Default_PROColor_LKUP[];
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int grp = 0;
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codon[3] = '\0';
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fptr = 0;
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save_name = malloc(80);
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strncpy(save_name, seq->name, 80);
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temp=(char*)Calloc(seq->seqlen+1,sizeof(char));
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for(i=0;i<seq->seqlen;i++)
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temp[i] = '-';
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if(letter_code == 1)
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{
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/*
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* Triple letter codes
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*/
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strcpy(seq->type,"TEXT");
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}
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else
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{
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/*
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* Single Letter Codes
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*/
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strcpy(seq->type , "PROT");
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}
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/*
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* Skip over r_frame valid characters (skip ' ','-','~')
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*/
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for(true_start=0,i=0; i<r_frame&&true_start<
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seq->seqlen;true_start++)
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{
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c=seq->c_elem[true_start];
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if(index(" -~",c) == NULL)
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i++;
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}
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for(pos=true_start;pos<seq->seqlen;pos++)
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{
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c=seq->c_elem[pos];
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if(index(" -~",c) == NULL)
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{
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c &= (255-32); /*upper case*/
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if(c == 'U') c = 'T';
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/*
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* We have a valid character...
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*/
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if(fptr == 0)
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start = pos;
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codon[fptr++] = c;
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/*
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* Translate the codon...
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*/
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if(fptr == 3)
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{
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/*
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* Place default code 'X' in case translation fails
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*/
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temp[start] = 'X';
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for(i=0;i<512;i+=2)
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if(strcmp(codon,table[i]) == 0)
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{
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if(letter_code == 1)
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{
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temp[start] = table[i+1][0];
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temp[start+1] = table[i+1][1];
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temp[start+2] = table[i+1][2];
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}
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else
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temp[start] = ThreeToOne
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(table[i+1]);
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i = 512;
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}
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fptr = 0;
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/*
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* Check to see if it is a valid ORF
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*/
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if((strncmp("Ter",&(temp[start]),3) == 0) ||
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(temp[start] == '*'))
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{
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/*
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* If the ORF is too small, clear it out...
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*/
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if(codon_count < min_frame)
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{
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/*
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* Should we seperate the groups out, or not?!?!
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*
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*/
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if (!sep)
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{
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/*
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* If reading from stop to stop, leave the elading stop codon
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*/
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if(temp[last_start]=='*' ||
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strncmp("Ter",&(temp[last_start]),3) == 0)
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for(i=last_start+3;i<start+3;i++)
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temp[i] = '-';
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/*
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* Otherwise, we are at the first coding region, no stop codon...
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*/
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else
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for(i=last_start;i<start+3;i++)
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temp[i] = '-';
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}
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else
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{
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for(i=0;i<seq->seqlen;i++)
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temp[i] = '-';
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||
|
|
}
|
||
|
|
}
|
||
|
|
else
|
||
|
|
{
|
||
|
|
if (sep)
|
||
|
|
{
|
||
|
|
sprintf(strtmp, "_%d", grp++);
|
||
|
|
strncat(seq->name, strtmp, 20);
|
||
|
|
save_c_elem = seq->c_elem;
|
||
|
|
seq->c_elem = temp;
|
||
|
|
WriteRecord(stdout,seq,NULL,0);
|
||
|
|
strncpy(seq->name, save_name, 80);
|
||
|
|
seq->c_elem = save_c_elem;
|
||
|
|
for(i=0;i<seq->seqlen;i++)
|
||
|
|
temp[i] = '-';
|
||
|
|
}
|
||
|
|
}
|
||
|
|
codon_count = 0;
|
||
|
|
last_start = start;
|
||
|
|
/*
|
||
|
|
* Don't bother continuing if too close to end to meat min_frame requirements
|
||
|
|
*
|
||
|
|
*/
|
||
|
|
if ((pos + (3 * min_frame)) > seq->seqlen)
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
else
|
||
|
|
codon_count++;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
Cfree(seq->c_elem);
|
||
|
|
if (!sep)
|
||
|
|
{
|
||
|
|
seq->c_elem = temp;
|
||
|
|
WriteRecord(stdout,seq,NULL,0);
|
||
|
|
}
|
||
|
|
Cfree(temp);
|
||
|
|
return;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
char ThreeToOne(s)
|
||
|
|
char s[];
|
||
|
|
{
|
||
|
|
extern char three_to_one[][5];
|
||
|
|
int j;
|
||
|
|
|
||
|
|
for(j=0;j<23;j++)
|
||
|
|
if(strncmp(s,three_to_one[j],3) == 0)
|
||
|
|
return(three_to_one[j][3]);
|
||
|
|
Warning("ThreeToOne, code not found");
|
||
|
|
return('*');
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
|