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/* COPYRIGHT 1998, Fred Hutchinson Cancer Research Center
fastaseqs.c Read a file of sequences and converts them to FASTA format
fastaseqs <input blocks file> <output file>
--------------------------------------------------------------------
1/15/98 J. Henikoff
====================================================================*/
#define EXTERN
#define MAXNAME 80 /* Maximum file name length */
#include <blocksprogs.h>
/*=======================================================================*/
/*
* main
*/
int main(argc, argv)
int argc;
char *argv[];
{
FILE *fin, *fout;
Sequence *seq;
char infile[MAXNAME], outfile[MAXNAME];
int db_type, seq_type, nseq;
if (argc < 2)
{
printf("COPYRIGHT 1998, Fred Hutchinson Cancer Research Center\n");
printf("fastaseqs: Converts a file of sequences to FASTA format\n");
printf("USAGE: fastaseqs <input> <output>\n");
printf(" <input> = input file of seqences in a common format\n");
printf(" <output> = output file of sequences in FASTA format\n");
}
/* ------------1st arg = file of sequences------------------------------*/
if (argc > 1)
strcpy(infile, argv[1]);
else
{
printf("\nEnter name of input sequence file: ");
fgets(infile, MAXNAME, stdin);
}
if ( (fin=fopen(infile, "r")) == NULL)
{
printf("\nCannot open file %s\n", infile);
exit(-1);
}
/* ------------2nd arg = output file -----------------------------------*/
if (argc > 2)
strcpy(outfile, argv[2]);
else
{
printf("\nEnter name of output file: ");
fgets(outfile, MAXNAME, stdin);
}
if ( (fout=fopen(outfile, "w")) == NULL)
{
printf("\nCannot open file %s\n", outfile);
exit(-1);
}
/*-----------------------------------------------------------------*/
db_type = type_dbs(fin, DbInfo);
if (db_type < 0) db_type = FLAT;
seq_type = UNKNOWN_SEQ;
seq_type = seq_type_dbs(fin, DbInfo, db_type, seq_type);
/*-----------------------------------------------------------------*/
/* Have to read all the sequences into memory */
rewind(fin);
nseq = 0;
while ( (seq = read_a_sequence(fin, db_type, seq_type)) != NULL)
{
nseq++;
output_sequence(seq, fout);
free_sequence(seq);
}
fclose(fin); fclose(fout);
printf("%d sequences read\n", nseq);
if (nseq > 0) exit(0);
else exit(-1);
} /* end of main */
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