translation.c

//
// Created by M on 28/03/2018.
//

#include "translation.h"

char * lerRNAFull(FILE *fp) {
    char cabecalho[TAMCABECALHO];
    char *rna;
    char aux;
    int qntLetras = 0;

    fgets(cabecalho, sizeof(cabecalho), fp); // Consome a primeira linha

    aux = (char) fgetc(fp);
    while(aux != EOF) { // Conta a quantidade de letras total do arquivo
        if(aux != '\n' && aux != '\t' && aux != ' ') {
            qntLetras++;
            aux = (char) fgetc(fp);
        }
        else
            aux = (char) fgetc(fp);
    }
    printf("O numero total de caratfcteres eh: %d \n", qntLetras);

    rewind(fp); // Retorna ao inicio do arquivo

    fgets(cabecalho, sizeof(cabecalho), fp); // Consome a primeira linha

    rna = (char *) malloc(sizeof(char) * (qntLetras+1)); //Aloca memoria para todas as letras

    for (int i = 0; i < qntLetras; i++) { // Salva as letras na memoria
        aux = (char) fgetc(fp);
        if(aux != '\n' && aux != '\t' && aux != ' ') {
            rna[i] = aux;
        }
        else {
            i--;
        }
    }
    rna[qntLetras] = '\0'; // Adiciona o caracter /0 ao final da cadeia de letras

    return rna; // Retorna ponteiro com a sequencia
}

char *readRNAPart(char *rna, int inicio, int fim) {
    char *rnaPart;
    int qntLetras;

    inicio -= 1;
    fim -= 1;
    qntLetras = (fim - inicio) + 1;

    printf("O numero parcial de caratfcteres eh: %d \n", qntLetras);
    if(qntLetras%3){
        printf("Quantidade de nucleotideos nao eh multiplo de tres.");
        return NULL;
    }

    rnaPart = (char *) malloc(sizeof(char) * (qntLetras+1)); //Aloca memoria para as letras necessarias

    for (int i = 0; i < qntLetras; i++) { // Salva as letras na memoria
        rnaPart[i] = rna[inicio+i];
    }

    rnaPart[qntLetras] = '\0'; // Adiciona o caracter /0 ao final da cadeia de letras

    printf("\n%s\n", rnaPart);

    return rnaPart;
}

char *gerarPolipeptideo(char *rna) {
    char *polipeptideo, codon[3];
    int cont = 0, j = 0;

    for (int i = 0; rna[i] != '\0' ; i++) {
        cont++;
    }

    polipeptideo = (char *) malloc(sizeof(char) * ((cont/3)+1) );
    printf("\ncontador no polipeptideo: %d\n", ((cont/3)+1) );

    for (int i = 0; rna[i] != '\0'; i += 3) {
        codon[0] = rna[i];
        codon[1] = rna[i+1];
        codon[2] = rna[i+2];

        polipeptideo[j] = codigoGenetico(codon);
        j++;
    }
    polipeptideo[cont/3] = '\0';

    return polipeptideo;
}

char * invertRNA(char *rna) {
    char *rnaAux;
    int  cont = 0;
    int i, j;
    j = 0;

    for (i = 0; rna[i] != '\0' ; i++) {
        cont++;
    }

    rnaAux = (char *) malloc(sizeof(char)*cont);

    rnaAux[cont] = '\0';
    cont -= 1;

    while (cont >= 0) {
        rnaAux[j] = rna[cont];
        j++;
        cont--;
    }

    printf("\nInvertido rnaAux: %s\n", rnaAux);
    return rnaAux;
}

void complementRNA(char * rna) {
    for (int i = 0; rna[i] != '\0' ; i++) {
        if (rna[i] == 'A') {
            rna[i] = 'T';
        } else if (rna[i] == 'T') {
            rna[i] = 'A';
        } else rna[i] = (char) (rna[i] == 'C' ? 'G' : 'C');
    }

    printf("\nrna complementar: %s\n", rna);
}

char codigoGenetico(char codon[]) {
    if( (!strncmp(codon, "GCT", 3)) || (!strncmp(codon, "GCC", 3)) || (!strncmp(codon, "GCA", 3)) || (!strncmp(codon, "GCG", 3))) {
        return 'A';
    } else if ( (!strncmp(codon, "CGT", 3)) || (!strncmp(codon, "CGC", 3)) || (!strncmp(codon, "CGA", 3)) || (!strncmp(codon, "CGG", 3)) || (!strncmp(codon, "AGA", 3)) || (!strncmp(codon, "AGG", 3))) {
        return 'R';
    } else if ( (!strncmp(codon, "AAT", 3)) || (!strncmp(codon, "AAC", 3))) {
        return 'N';
    } else if ( (!strncmp(codon, "GAT", 3)) || (!strncmp(codon, "GAC", 3))) {
        return 'D';
    } else if ( (!strncmp(codon, "TGT", 3)) || (!strncmp(codon, "TGC", 3))) {
        return 'C';
    } else if ( (!strncmp(codon, "CAA", 3)) || (!strncmp(codon, "CAG", 3))) {
        return 'Q';
    } else if ( (!strncmp(codon, "GAA", 3)) || (!strncmp(codon, "GAG", 3))) {
        return 'E';
    } else if ( (!strncmp(codon, "GGT", 3)) || (!strncmp(codon, "GGC", 3)) || (!strncmp(codon, "GGA", 3)) || (!strncmp(codon, "GGG", 3))) {
        return 'G';
    } else if ( (!strncmp(codon, "CAT", 3)) || (!strncmp(codon, "CAC", 3))) {
        return 'H';
    } else if ( (!strncmp(codon, "ATT", 3)) || (!strncmp(codon, "ATC", 3)) || (!strncmp(codon, "ATA", 3))) {
        return 'I';
    } else if ( (!strncmp(codon, "TTA", 3)) || (!strncmp(codon, "TTG", 3)) || (!strncmp(codon, "CTT", 3)) || (!strncmp(codon, "CTC", 3)) || (!strncmp(codon, "CTA", 3)) || (!strncmp(codon, "CTG", 3))) {
        return 'L';
    } else if ( (!strncmp(codon, "AAA", 3)) || (!strncmp(codon, "AAG", 3))) {
        return 'K';
    } else if ( (!strncmp(codon, "ATG", 3))) {
        return 'M';
    } else if ( (!strncmp(codon, "TTT", 3)) || (!strncmp(codon, "TTC", 3))) {
        return 'F';
    } else if( (!strncmp(codon, "CCT", 3)) || (!strncmp(codon, "CCC", 3)) || (!strncmp(codon, "CCA", 3)) || (!strncmp(codon, "CCG", 3))) {
        return 'P';
    } else if ( (!strncmp(codon, "TCT", 3)) || (!strncmp(codon, "TCC", 3)) || (!strncmp(codon, "TCA", 3)) || (!strncmp(codon, "TCG", 3)) || (!strncmp(codon, "AGT", 3)) || (!strncmp(codon, "AGC", 3))) {
        return 'S';
    } else if( (!strncmp(codon, "ACT", 3)) || (!strncmp(codon, "ACC", 3)) || (!strncmp(codon, "ACA", 3)) || (!strncmp(codon, "ACG", 3))) {
        return 'T';
    } else if( (!strncmp(codon, "TGG", 3))) {
        return 'W';
    } else if( (!strncmp(codon, "TAT", 3)) || (!strncmp(codon, "TAC", 3))) {
        return 'Y';
    } else if( (!strncmp(codon, "GTT", 3)) || (!strncmp(codon, "GTC", 3)) || (!strncmp(codon, "GTA", 3)) || (!strncmp(codon, "GTG", 3))) {
        return 'V';
    } else if( (!strncmp(codon, "TAA", 3)) || (!strncmp(codon, "TAG", 3)) || (!strncmp(codon, "TGA", 3))) {
        return '\0';
    }
}

float calcMassa(char *polipept) {
    float peso;
    peso = 0;
    for (int i = 0; polipept[i] != '\0'; i++) {
        if(polipept[i] == 'A') {
            peso += 89.0935;
        } else if(polipept[i] == 'C') {
            peso += 121.159;
        } else if(polipept[i] == 'D') {
            peso += 133.1032;
        } else if(polipept[i] == 'E') {
            peso += 174.1299;
        } else if(polipept[i] == 'F') {
            peso += 165.19;
        } else if(polipept[i] == 'G') {
            peso += 75.0669;
        } else if(polipept[i] == 'H') {
            peso += 155.1502;
        } else if(polipept[i] == 'I') {
            peso += 131.1736;
        } else if(polipept[i] == 'K') {
            peso += 146.1882;
        } else if(polipept[i] == 'L') {
            peso += 131.1736;
        } else if(polipept[i] == 'M') {
            peso += 149.2124;
        } else if(polipept[i] == 'N') {
            peso += 132.1184;
        } else if(polipept[i] == 'P') {
            peso += 115.131;
        } else if(polipept[i] == 'R') {
            peso += 174.2017;
        } else if(polipept[i] == 'S') {
            peso += 105.093;
        } else if(polipept[i] == 'T') {
            peso += 119.1197;
        } else if(polipept[i] == 'V') {
            peso += 117.1469;
        } else if(polipept[i] == 'W') {
            peso += 204.2262;
        } else if(polipept[i] == 'Y') {
            peso += 181.1894;
        }
    }
    return peso;
}

int calcFrame(int posicInic) {
    int frame;

    frame = posicInic % 3 + 1;

    return frame;
}

int buscaPromotor(char *rna, int posicInic, int utr) {

    char aux[utr], promotor[utr];
    int tamAux = 0, tamPromotor = 0;
    int contATAux = 0, contATPromotor = 0;
    int qntAAux = 0, qntTAux = 0;
    int qntAPromotor = 0, qntTPromotor = 0;
    int posicPromotor = 0;


    for(int i = posicInic - 1; i >= posicInic - utr; i--) {
        if(rna[i] == 'A' || rna[i] == 'T') {
            aux[tamAux] = rna[i];
            tamAux++;
        } else {
            if(tamAux > tamPromotor) {
                strncpy(promotor, aux, (size_t) tamAux);
                tamPromotor = tamAux;
                promotor[tamPromotor] = '\0';
                posicPromotor = i;
                tamAux = 0;

            } else if(tamAux == tamPromotor) {
                for (int j = 0; j < tamAux; j+=2) {
                    if(!strncmp(aux, "AT",2) || !strncmp(aux, "TA",2)){
                        contATAux++;
                    }
                }
                for (int k = 0; k < tamPromotor; k+=2) {
                    if(!strncmp(promotor, "AT",2) || !strncmp(aux, "TA",2)){
                        contATPromotor++;
                    }
                }
                if(contATAux > contATPromotor) {
                    strncpy(promotor, aux, (size_t) tamAux);
                    tamPromotor = tamAux;
                    promotor[tamPromotor] = '\0';
                    posicPromotor = i;
                    tamAux = contATAux = contATPromotor = 0;
                } else if(contATAux == contATPromotor) {
                    for (int j = 0; j < tamAux; j++) {
                        if(aux[j] == 'A') {
                            qntAAux++;
                        } else{
                            qntTAux++;
                        }
                    }
                    for (int k = 0; k < tamPromotor; k++) {
                        if(aux[k] == 'A') {
                            qntAPromotor++;
                        } else{
                            qntTPromotor++;
                        }
                    }
                    if((qntAAux/qntTAux)>(qntAPromotor/qntTPromotor)) {
                        strncpy(promotor, aux, (size_t) tamAux);
                        tamPromotor = tamAux;
                        promotor[tamPromotor] = '\0';
                        posicPromotor = i;
                    }
                }
            }
        }
    }

    promotor[tamPromotor] = '\0';

    printf("\nPromotor: %s", promotor);
    printf("\nPosicao inicial do promotor: %d", posicPromotor);

    return posicPromotor;
}

char **calcFragmentos(int *qntFragmentos, char *rna, char *enzimaRestricao) { // Retorna o numero de fragmentos //

    int qntEnzima = 0, qntBases = 0;
    char **fragmentos = NULL;

    qntEnzima = strlen(enzimaRestricao);

    for (int i = 0; rna[i] != '\0'; i++) {
        if(!strncmp((const char *) rna + i, enzimaRestricao, (size_t) qntEnzima)) {
            *qntFragmentos += 1;
        }
    }

    *qntFragmentos += 1;

    fragmentos = (char **) malloc(sizeof(char *) * (*qntFragmentos));

    for (int i = 0, k = 0; k < *qntFragmentos; k++) {

        for (int j = i; (strncmp((const char *) rna + j, enzimaRestricao, (size_t) qntEnzima) ) != 0 && rna[j] != '\0'; j++) {
            qntBases++;
        }

        qntBases++;

        fragmentos[k] = (char *) malloc(sizeof(char) * qntBases + 1);
        fragmentos[k][qntBases] = '\0';
        strncpy(fragmentos[k], rna + i, (size_t) qntBases);
        i += qntBases;
        qntBases = 0;
    }

    return fragmentos;
}

void leArqReads(structRead reads[], FILE * fp) {
    int lixo;
    for (int i = 0; i < QNTREADS; i++) {
        fscanf(fp, "%d %u %u %c\n", lixo, reads[i].inicio, reads[i].fim, reads[i].fita);
        reads[i].contigRead = 0;
    }
}