File size: 3,343 Bytes
35cdf53 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | --- hmmer-3.4/src/jackhmmer.c
+++ hmmer-3.4/src/jackhmmer.c
@@ -73,6 +73,7 @@ static ESL_OPTIONS options[] = {
{ "--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 },
{ "--textw", eslARG_INT, "120", NULL, "n>=120", NULL, NULL, "--notextw", "set max width of ASCII text output lines", 2 },
+ { "--seq_limit", eslARG_INT, NULL, NULL, NULL, NULL, NULL, "--seq_limit", "if set, truncate all hits after this value is reached", 2 },
/* Control of scoring system */
{ "--popen", eslARG_REAL, "0.02", NULL, "0<=x<0.5",NULL, NULL, NULL, "gap open probability", 3 },
{ "--pextend", eslARG_REAL, "0.4", NULL, "0<=x<1", NULL, NULL, NULL, "gap extend probability", 3 },
@@ -298,6 +299,7 @@ output_header(FILE *ofp, ESL_GETOPTS *go
if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimited\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--textw") && fprintf(ofp, "# max ASCII text line length: %d\n", esl_opt_GetInteger(go, "--textw")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+ if (esl_opt_IsUsed(go, "--seq_limit") && fprintf(ofp, "# set max sequence hits to return: %d\n", esl_opt_GetInteger(go, "--seq_limit")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--popen") && fprintf(ofp, "# gap open probability: %f\n", esl_opt_GetReal (go, "--popen")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--pextend") && fprintf(ofp, "# gap extend probability: %f\n", esl_opt_GetReal (go, "--pextend")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--mx") && fprintf(ofp, "# subst score matrix (built-in): %s\n", esl_opt_GetString (go, "--mx")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
@@ -674,6 +676,13 @@ serial_master(ESL_GETOPTS *go, struct cf
/* Print the results. */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
+ /* Limit the number of hits if specified. */
+ if (esl_opt_IsOn(go, "--seq_limit"))
+ {
+ int seq_limit = esl_opt_GetInteger(go, "--seq_limit");
+ info->th->N = ESL_MIN(info->th->N, seq_limit);
+ }
+
p7_tophits_CompareRanking(info->th, kh, &nnew_targets);
p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); |