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Prepend sequence index if names non-unique in aligned fasta format #29

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Prepend sequence index if names non-unique in aligned fasta format #29

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16 changes: 15 additions & 1 deletion esl_msafile_afa.c
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Original file line number Diff line number Diff line change
Expand Up @@ -279,10 +279,24 @@ esl_msafile_afa_Write(FILE *fp, const ESL_MSA *msa)
int64_t pos;
char buf[61];
int acpl; /* actual number of characters per line */
int make_uniquenames = FALSE; /* TRUE if we force names to be unique */
int status;
int tmpnseq;
int uniqwidth;

status = esl_msa_CheckUniqueNames(msa);
if (status == eslFAIL) {
make_uniquenames = TRUE;
for (tmpnseq = msa->nseq; tmpnseq; tmpnseq /= 10) uniqwidth++; /* how wide the uniqizing numbers need to be */
}

for (i = 0; i < msa->nseq; i++)
{
if (fprintf(fp, ">%s", msa->sqname[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
if (make_uniquenames) {
if (fprintf(fp, ">%0*d/%s", uniqwidth, i, msa->sqname[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
} else {
if (fprintf(fp, ">%s", msa->sqname[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
}
if (msa->sqacc != NULL && msa->sqacc[i] != NULL) { if (fprintf(fp, " %s", msa->sqacc[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed"); }
if (msa->sqdesc != NULL && msa->sqdesc[i] != NULL) { if (fprintf(fp, " %s", msa->sqdesc[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed"); }
if (fputc('\n', fp) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
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