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Adds -F option to hmmc2 to report hits as Stockholm format MSA for an… #272

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Adds -F option to hmmc2 to report hits as Stockholm format MSA for an… #272

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35 changes: 30 additions & 5 deletions src/hmmc2.c
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@
#define THRESHOPTS "-E,-T,--domE,--domT,--incE,--incT,--incdomE,--incdomT,--cut_ga,--cut_nc,--cut_tc"

static ESL_OPTIONS searchOpts[] = {
/* name type default env range toggles reqs incomp help docgroup*/
/* Control of output */
/* name type default env range toggles reqs incomp help docgroup*/
/* Control of output */
{ "--acc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "prefer accessions over names in output", 2 },
{ "--noali", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "don't output alignments, so output is smaller", 2 },
{ "--notextw", eslARG_NONE, NULL, NULL, NULL, NULL, NULL, "--textw", "unlimit ASCII text output line width", 2 },
Expand Down Expand Up @@ -168,6 +168,7 @@ usage(char *pgm)
if (fprintf(stderr, "Usage: %s [-i addr] [-p port] [-A] [-S]\n", pgm) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(stderr, " -S : print sequence scores\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(stderr, " -A : print sequence alignments\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(stderr, " -F : print flattened hit alignment\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(stderr, " -i addr : ip address running daemon (default: 127.0.0.1)\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(stderr, " -p port : port daemon listens to clients on (default: 51371)\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
exit(1);
Expand All @@ -184,6 +185,7 @@ int main(int argc, char *argv[])
char opts[MAX_READ_LEN];
int seqlen;

int msa;
int ali;
int scores;

Expand Down Expand Up @@ -215,6 +217,7 @@ int main(int argc, char *argv[])
serv_port = SERVER_PORT;
scores = 0;
ali = 0;
msa = 0;

i = 1;
while (i < argc) {
Expand Down Expand Up @@ -244,6 +247,9 @@ int main(int argc, char *argv[])
case 'S':
scores = 1;
break;
case 'F':
msa = 1;
break;
default:
usage(argv[0]);
}
Expand Down Expand Up @@ -535,11 +541,30 @@ int main(int argc, char *argv[])
/* adjust the reported and included hits */
//th->is_sorted = FALSE;
//p7_tophits_Sort(th);
/* Print the results. */
if (scores) { p7_tophits_Targets(stdout, th, pli, 120); fprintf(stdout, "\n\n"); }
if (ali) { p7_tophits_Domains(stdout, th, pli, 120); fprintf(stdout, "\n\n"); }
p7_pli_Statistics(stdout, pli, w);

if (msa) {
ESL_MSA *msa = NULL;
// code taken from -A output routine of hmmsearch.c - JBP

if (p7_tophits_Alignment(th, abc, NULL, NULL, 0, p7_ALL_CONSENSUS_COLS, &msa) == eslOK)
{
// TODO insert query name in alignment
esl_msa_SetName (msa, "seqName", -1); // hmm->name, -1);
// esl_msa_SetAccession(msa, hmm->acc, -1); // hmm->acc, -1);
//esl_msa_SetDesc (msa, hmm->desc, -1); // hmm->desc, -1);
esl_msa_FormatAuthor(msa, "hmmsearch (HMMER %s)", HMMER_VERSION);

// write to stdout
esl_msafile_Write(stdout, msa, eslMSAFILE_STOCKHOLM); // could be pfam here instead
}
esl_msa_Destroy(msa);
}

p7_pli_Statistics(stdout, pli, w);

p7_pipeline_Destroy(pli);
p7_tophits_Destroy(th);
Expand All @@ -557,7 +582,7 @@ int main(int argc, char *argv[])
if (hmm) p7_hmm_Destroy(hmm);
if (sq) esl_sq_Destroy(sq);

}
}
}

free(seq);
Expand Down