source: branches/port5/CONVERTALN/phylip.c

#include <stdio.h>
#include "convert.h"
#include "global.h"

#include <assert.h>
#include <errno.h>


/* ---------------------------------------------------------------
 *   Function init_phylip().
 *       Initialize genbank entry.
 */
void init_phylip()  {

}
/* ---------------------------------------------------------------
 *  Function to_phylip()
 *      Convert from some format to PHYLIP format.
 */
void to_phylip(inf, outf, informat,readstdin)
     char *inf, *outf;
     int   informat;
     int   readstdin;
{
    FILE        *IFP, *ofp;
    FILE_BUFFER  ifp;
    int          maxsize, current, total_seq;
    int          out_of_memory, indi;
    char         temp[TOKENNUM], eof;
    char        *name;

    if((IFP=fopen(inf, "r"))==NULL) {
        sprintf(temp, "Cannot open input file %s, exit\n", inf);
        error(64, temp);
    }
    ifp              = create_FILE_BUFFER(inf, IFP);
    if(Lenstr(outf) <= 0) {
        ofp = stdout;
        assert(0); // can't use stdout (because rewind is used below)
        error(140, "Cannot write to standard output, EXIT\n");
    }
    else if((ofp=fopen(outf, "w"))==NULL)   {
        sprintf(temp, "Cannot open output file %s, exit\n", outf);
        error(117, temp);
    }
    maxsize = 1;
    out_of_memory = 0;
    name = NULL;
    init();
    init_phylip();
    total_seq = 0;
    do  {
        if(informat==ALMA)  {
            init_alma();
            eof=alma_in(ifp);
        } else if(informat==GENBANK)    {
            init_genbank();
            eof=genbank_in_locus(ifp);
        } else if(informat==EMBL||informat==PROTEIN)    {
            init_embl();
            eof=embl_in_id(ifp);
        } else if(informat==MACKE)  {
            init_macke();
            eof=macke_in_name(ifp);
        } else error(34, "UNKNOW input format when converting to PHYLIP format.");
        if(eof==EOF) break;
        if(informat==ALMA)  {
            alma_key_word(data.alma.id, 0, temp, TOKENNUM);
        } else if(informat==GENBANK)    {
            genbank_key_word(data.gbk.locus, 0, temp, TOKENNUM);
        } else if(informat==EMBL||informat==PROTEIN)    {
            embl_key_word(data.embl.id, 0, temp, TOKENNUM);
        } else if(informat==MACKE)  {
            Cpystr(temp, data.macke.seqabbr);
        } else error(119, "UNKNOW input format when converting to PHYLIP format.");
        total_seq++;

        if((name = Dupstr(temp))==NULL&&temp!=NULL) { out_of_memory=1; break; }
        if(data.seq_length>maxsize) maxsize = data.seq_length;

        if (!realloc_sequence_data(total_seq)) { out_of_memory = 1; break; }

        data.ids[total_seq-1]     = name;
        data.seqs[total_seq-1]    = (char*)Dupstr(data.sequence);
        data.lengths[total_seq-1] = Lenstr(data.sequence);
    } while(!out_of_memory);

    if(out_of_memory)   {   /* cannot hold all seqs into mem. */
        fprintf(stderr,
                "Rerun the conversion throught one seq. by one seq. base.\n");
        destroy_FILE_BUFFER(ifp); fclose(ofp);
        to_phylip_1x1(inf, outf, informat);
        return;
    }
    current         = 0;
    int headersize1 = fprintf(ofp, "%8d %8d", maxsize, current);
    if (readstdin){
        int c;
        int spaced = 0;
        while (1) {
            c = getchar();
            if (c == EOF) break; /* read all from stdin now (not only one line)*/
            /*      if (c == EOF||c=='\n') break; */
            if (!spaced) {
                fputc(' ', ofp);
                spaced = 1;
            }
            fputc(c,ofp);
        }

    }
    fprintf(ofp,"\n");

    while(maxsize>current)  {
        for(indi=0; indi<total_seq; indi++) {
            phylip_print_line(data.ids[indi], data.seqs[indi], data.lengths[indi], current, ofp);
        }
        if(current==0) current +=(SEQLINE-10);
        else current += SEQLINE;
        if(maxsize>current) fprintf(ofp, "\n");
    }
    /* rewrite output header */
    errno = 0;
    rewind(ofp);
    assert(errno == 0);
    if (errno) {
        perror("rewind error");
        sprintf(temp, "Failed to rewind file (errno=%i), EXIT\n", errno);
        error(141, temp);
    }

    int headersize2 = fprintf(ofp, "%8d %8d", total_seq, maxsize);

    destroy_FILE_BUFFER(ifp); fclose(ofp);

    if (headersize1 != headersize2) {
        sprintf(temp, "Failed to rewrite header (headersize differs: %i != %i), EXIT\n", headersize1, headersize2);
        assert(0);
        error(142, temp);
    }

#ifdef log
    fprintf(stderr, "Total %d sequences have been processed\n", total_seq);
#endif
}
/* ---------------------------------------------------------------
 *   Function to_phylip_1x1()
 *       Convert from one format to PHYLIP format, one seq by one seq.
 */
void
to_phylip_1x1(inf, outf, informat)
     char   *inf, *outf;
     int    informat;
{
    FILE        *IFP, *ofp;
    FILE_BUFFER  ifp;
    int          maxsize, current, total_seq;
    char         temp[TOKENNUM], eof;
    char        *name;

    if((IFP=fopen(inf, "r"))==NULL) {
        sprintf(temp, "Cannot open input file %s, exit\n", inf);
        error(123, temp);
    }
    ifp              = create_FILE_BUFFER(inf, IFP);
    if(Lenstr(outf) <= 0)   ofp = stdout;
    else if((ofp=fopen(outf, "w"))==NULL)   {
        sprintf(temp, "Cannot open output file %s, exit\n", outf);
        error(124, temp);
    }
    maxsize = 1; current = 0;
    name = NULL;
    fprintf(ofp, "%4d %4d\n", maxsize, current);
    while(maxsize>current)  {
        init();
        FILE_BUFFER_rewind(ifp);
        total_seq = 0;
        do  {   /* read in one sequence */
            init_phylip();
            if(informat==ALMA)  {
                init_alma();
                eof=alma_in(ifp);
            } else if(informat==GENBANK)    {
                init_genbank();
                eof=genbank_in_locus(ifp);
            } else if(informat==EMBL||informat==PROTEIN)    {
                init_embl();
                eof=embl_in_id(ifp);
            } else if(informat==MACKE)  {
                init_macke();
                eof=macke_in_name(ifp);
            } else error(128, "UNKNOWN input format when converting to PHYLIP format.");
            if(eof==EOF) break;
            if(informat==ALMA)  {
                alma_key_word(data.alma.id, 0, temp, TOKENNUM);
            } else if(informat==GENBANK)    {
                genbank_key_word(data.gbk.locus, 0, temp, TOKENNUM);
            } else if(informat==EMBL||informat==PROTEIN)    {
                embl_key_word(data.embl.id, 0, temp, TOKENNUM);
            } else if(informat==MACKE)  {
                macke_key_word(data.macke.name, 0, temp, TOKENNUM);
            } else error(130, "UNKNOWN input format when converting to PHYLIP format.");
            Freespace(&name);
            name = Dupstr(temp);
            if(data.seq_length>maxsize) maxsize = data.seq_length;
            phylip_print_line(name, data.sequence, 0, current, ofp);
            total_seq++;
        } while(1);
        if(current==0)  current += (SEQLINE-10);
        else current += SEQLINE;
        if(maxsize>current) fprintf(ofp, "\n");
    }   /* print block by block */

    rewind(ofp);
    fprintf(ofp, "%4d %4d", total_seq, maxsize);

    destroy_FILE_BUFFER(ifp); fclose(ofp);

#ifdef log
    fprintf(stderr, "Total %d sequences have been processed\n", total_seq);
#endif

}
/* --------------------------------------------------------------
 *  Function phylip_print_line().
 *      Print phylip line.
 */
void
phylip_print_line(name, sequence, seq_length, index, fp)
     char *name, *sequence;
     int   seq_length;
     int    index;
     FILE   *fp;
{
    int indi, indj, length, bnum;

    if(index==0)    {
        if(Lenstr(name)>10) {
            /* truncate id length of seq ID is greater than 10 */
            for(indi=0; indi<10; indi++) fputc(name[indi], fp);
            bnum = 1;
        } else  {
            fprintf(fp, "%s", name);
            bnum = 10 - Lenstr(name)+1;
        }
        /* fill in blanks to make up 10 chars for ID. */
        for(indi=0; indi<bnum; indi++) fputc(' ', fp);
        length = SEQLINE - 10;
    } else if(index>=data.seq_length) length = 0;
    else length = SEQLINE;

    if (seq_length == 0) seq_length = Lenstr(sequence);
    for(indi=indj=0; indi<length; indi++) {
        if((index+indi)<seq_length) {
            char c= sequence[index+indi];
            if (c=='.') c= '?';
            fputc(c,fp);
            indj++;
            if(indj==10 && (index+indi)<(seq_length-1) && indi<(length-1)) {
                fputc(' ', fp);
                indj=0;
            }
        } else break;
    }
    fprintf(fp, "\n");
}