int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
ESL_RANDOMNESS *r = NULL; /* random number generator */
FILE *ofp = NULL; /* data output stream */
int outfmt = eslSQFILE_FASTA;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK)
cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK)
cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") )
cmdline_help(argv[0], go);
/* Open the output data file, if any */
if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Initialize */
r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
/* Hand off execution to one of the three modes */
if (esl_opt_GetBoolean(go, "-A")) /* Alignment shuffling */
{
if (esl_opt_ArgNumber(go) != 1)
cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
msa_shuffling(go, r, ofp, outfmt);
}
else if (esl_opt_GetBoolean(go, "-G")) /* Sequence generation */
{
if (esl_opt_ArgNumber(go) != 0)
cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
seq_generation(go, r, ofp, outfmt);
}
else if (esl_opt_GetBoolean(go, "-S")) /* Sequence shuffling */
{
if (esl_opt_ArgNumber(go) != 1)
cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
seq_shuffling(go, r, ofp, outfmt);
}
if (esl_opt_GetString(go, "-o") != NULL) fclose(ofp);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
/*
* Print usage info.
*/
static void
usage(FILE *out)
{
const char *help_str;
fprintf(out, "Usage: %s [OPTIONS]\n", cmdline_progname);
fprintf(out, "\n");
while ((help_str = cmdline_help(mced_opts))) {
fprintf(out, " %s\n", help_str);
}
fprintf(out, "\n");
}
/* Get args using getopt */
int cmdline_getargs(int argc, char* argv[], nanoturingCmdlineArgs* cmdline) {
char options;
if (argc <= 2)
cmdline_help(argv[0],-1);
else if (strcmp(argv[1], "--help") == 0)
cmdline_help(argv[0],0);
while((options = getopt(argc,argv, "f:t:c:vi")) != -1)
{
switch(options)
{
case 'f':
cmdline->filename = optarg;
break;
case 't':
cmdline->tape = optarg;
break;
case 'c':
cmdline->count_symbol = optarg[0];
break;
case 'i':
cmdline->interact = 1;
break;
case 'v':
cmdline->verbose = 1;
break;
default :
fprintf(stderr,"Parsing error\n");
cmdline_help(argv[0],-1);
break;
}
}
return 0;
}
int main(int argc, char **argv)
{
if (argc <= 1)
cmdline_help();
init_windows();
init_buffers();
for (argv++; *argv != NULL ; argv++)
current_buf = load_buffer(*argv);
paint_buffer(current_buf);
statusprintf("%s", current_buf->name);
refresh();
input_loop();
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL;
char *keyfile = NULL;
char *tabfile = NULL;
ESL_KEYHASH *kh = esl_keyhash_Create();
int nkeys = 0;
ESL_DMATRIX *D = NULL;
ESL_TREE *T = NULL;
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], go, "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], go, "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], go, "Incorrect number of command line arguments.\n");
keyfile = esl_opt_GetArg(go, 1);
tabfile = esl_opt_GetArg(go, 2);
read_keyfile(go, keyfile, kh);
nkeys = esl_keyhash_GetNumber(kh);
D = esl_dmatrix_Create(nkeys, nkeys);
read_tabfile(go, tabfile, kh, D);
esl_tree_SingleLinkage(D, &T);
//esl_tree_WriteNewick(stdout, T);
output_clusters(go, T, kh);
esl_tree_Destroy(T);
esl_dmatrix_Destroy(D);
esl_keyhash_Destroy(kh);
esl_getopts_Destroy(go);
return 0;
}
int main(int argc, char** argv)
{
struct fpga_model model;
const char *param_clock_pin, *param_led_pin;
int iob_clk_y, iob_clk_x, iob_clk_type_idx;
int iob_led_y, iob_led_x, iob_led_type_idx;
if (cmdline_help(argc, argv)) {
printf("\n");
return 0;
}
if (!(param_clock_pin = cmdline_strvar(argc, argv, "clock_pin")))
param_clock_pin = "IO_L30N_GCLK0_USERCCLK_2";
if (!(param_led_pin = cmdline_strvar(argc, argv, "led_pin")))
param_led_pin = "IO_L48P_D7_2";
fpga_build_model(&model, cmdline_part(argc, argv),
cmdline_package(argc, argv));
fpga_find_iob(&model, xc6_find_pkg_pin(model.pkg, param_clock_pin),
&iob_clk_y, &iob_clk_x, &iob_clk_type_idx);
fdev_iob_input(&model, iob_clk_y, iob_clk_x, iob_clk_type_idx,
IO_LVCMOS33);
fpga_find_iob(&model, xc6_find_pkg_pin(model.pkg, param_led_pin),
&iob_led_y, &iob_led_x, &iob_led_type_idx);
fdev_iob_output(&model, iob_led_y, iob_led_x, iob_led_type_idx,
IO_LVCMOS25);
fdev_iob_slew(&model, iob_led_y, iob_led_x, iob_led_type_idx,
SLEW_QUIETIO);
fdev_iob_drive(&model, iob_led_y, iob_led_x, iob_led_type_idx,
8);
write_floorplan(stdout, &model, FP_DEFAULT);
return fpga_free_model(&model);
}
int main(int argc, char** argv)
{
struct fpga_model model;
int param_bits;
const char *param_clock_pin, *param_led_pin;
int iob_clk_y, iob_clk_x, iob_clk_type_idx;
int iob_led_y, iob_led_x, iob_led_type_idx;
int logic_y, logic_x, logic_type_idx;
struct fpgadev_logic logic_cfg;
net_idx_t net;
if (cmdline_help(argc, argv)) {
printf( " %*s [-Dbits=14|23]\n"
" %*s [-Dclock_pin=P55|...]\n"
" %*s [-Dled_pin=P48|...]\n"
"\n", (int) strlen(*argv), "",
(int) strlen(*argv), "", (int) strlen(*argv), "");
return 0;
}
if (!(param_bits = cmdline_intvar(argc, argv, "bits")))
param_bits = 14;
if (!(param_clock_pin = cmdline_strvar(argc, argv, "clock_pin")))
param_clock_pin = "P55";
if (!(param_led_pin = cmdline_strvar(argc, argv, "led_pin")))
param_led_pin = "P48";
fpga_build_model(&model, cmdline_part(argc, argv),
cmdline_package(argc, argv));
fpga_find_iob(&model, param_clock_pin, &iob_clk_y, &iob_clk_x, &iob_clk_type_idx);
fdev_iob_input(&model, iob_clk_y, iob_clk_x, iob_clk_type_idx,
IO_LVCMOS33);
fpga_find_iob(&model, param_led_pin, &iob_led_y, &iob_led_x, &iob_led_type_idx);
fdev_iob_output(&model, iob_led_y, iob_led_x, iob_led_type_idx,
IO_LVCMOS25);
fdev_iob_slew(&model, iob_led_y, iob_led_x, iob_led_type_idx,
SLEW_QUIETIO);
fdev_iob_drive(&model, iob_led_y, iob_led_x, iob_led_type_idx,
8);
logic_y = 58;
logic_x = 13;
logic_type_idx = DEV_LOG_M_OR_L;
CLEAR(logic_cfg);
logic_cfg.a2d[LUT_A].lut6 = "(A6+~A6)*(~A5)";
logic_cfg.a2d[LUT_A].lut5 = "1";
logic_cfg.a2d[LUT_A].cy0 = CY0_O5;
logic_cfg.a2d[LUT_A].ff = FF_FF;
logic_cfg.a2d[LUT_A].ff_mux = MUX_XOR;
logic_cfg.a2d[LUT_A].ff_srinit = FF_SRINIT0;
logic_cfg.a2d[LUT_B].lut6 = "(A6+~A6)*(A5)";
logic_cfg.a2d[LUT_B].lut5 = "0";
logic_cfg.a2d[LUT_B].cy0 = CY0_O5;
logic_cfg.a2d[LUT_B].ff = FF_FF;
logic_cfg.a2d[LUT_B].ff_mux = MUX_XOR;
logic_cfg.a2d[LUT_B].ff_srinit = FF_SRINIT0;
logic_cfg.a2d[LUT_C].lut6 = "(A6+~A6)*(A5)";
logic_cfg.a2d[LUT_C].lut5 = "0";
logic_cfg.a2d[LUT_C].cy0 = CY0_O5;
logic_cfg.a2d[LUT_C].ff = FF_FF;
logic_cfg.a2d[LUT_C].ff_mux = MUX_XOR;
logic_cfg.a2d[LUT_C].ff_srinit = FF_SRINIT0;
logic_cfg.a2d[LUT_D].lut6 = "(A6+~A6)*(A5)";
logic_cfg.a2d[LUT_D].lut5 = "0";
logic_cfg.a2d[LUT_D].cy0 = CY0_O5;
logic_cfg.a2d[LUT_D].ff = FF_FF;
logic_cfg.a2d[LUT_D].ff_mux = MUX_XOR;
logic_cfg.a2d[LUT_D].ff_srinit = FF_SRINIT0;
logic_cfg.clk_inv = CLKINV_CLK;
logic_cfg.sync_attr = SYNCATTR_ASYNC;
logic_cfg.precyinit = PRECYINIT_0;
logic_cfg.cout_used = 1;
fdev_logic_setconf(&model, logic_y, logic_x, logic_type_idx, &logic_cfg);
logic_y = 57;
logic_cfg.precyinit = 0;
logic_cfg.a2d[LUT_A].lut6 = "(A6+~A6)*(A5)";
logic_cfg.a2d[LUT_A].lut5 = "0";
fdev_logic_setconf(&model, logic_y, logic_x, logic_type_idx, &logic_cfg);
logic_y = 56;
fdev_logic_setconf(&model, logic_y, logic_x, logic_type_idx, &logic_cfg);
logic_y = 55;
logic_cfg.cout_used = 0;
logic_cfg.a2d[LUT_C].lut6 = "A5";
logic_cfg.a2d[LUT_C].lut5 = 0;
logic_cfg.a2d[LUT_C].cy0 = 0;
logic_cfg.a2d[LUT_C].ff = FF_FF;
logic_cfg.a2d[LUT_C].ff_mux = MUX_XOR;
logic_cfg.a2d[LUT_C].ff_srinit = FF_SRINIT0;
CLEAR(logic_cfg.a2d[LUT_D]);
fdev_logic_setconf(&model, logic_y, logic_x, logic_type_idx, &logic_cfg);
// clock to logic devs
fnet_new(&model, &net);
fnet_add_port(&model, net, iob_clk_y, iob_clk_x, DEV_IOB,
iob_clk_type_idx, IOB_OUT_I);
fnet_add_port(&model, net, 55, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CLK);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CLK);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CLK);
fnet_add_port(&model, net, 58, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CLK);
fnet_route(&model, net);
// vcc to logic devs
fnet_new(&model, &net);
fnet_add_port(&model, net, 55, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_A6);
fnet_add_port(&model, net, 55, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_B6);
fnet_vcc_gnd(&model, net, /*is_vcc*/ 1);
fnet_new(&model, &net);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_A6);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_B6);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_C6);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_D6);
fnet_vcc_gnd(&model, net, /*is_vcc*/ 1);
fnet_new(&model, &net);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_A6);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_B6);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_C6);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_D6);
fnet_vcc_gnd(&model, net, /*is_vcc*/ 1);
fnet_new(&model, &net);
fnet_add_port(&model, net, 58, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_A6);
fnet_add_port(&model, net, 58, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_B6);
fnet_add_port(&model, net, 58, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_C6);
fnet_add_port(&model, net, 58, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_D6);
fnet_vcc_gnd(&model, net, /*is_vcc*/ 1);
// carry chain
fnet_new(&model, &net);
fnet_add_port(&model, net, 55, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CIN);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LO_COUT);
fnet_route(&model, net);
fnet_new(&model, &net);
fnet_add_port(&model, net, 56, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CIN);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LO_COUT);
fnet_route(&model, net);
fnet_new(&model, &net);
fnet_add_port(&model, net, 57, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_CIN);
fnet_add_port(&model, net, 58, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LO_COUT);
fnet_route(&model, net);
// bit chain
{
int out_pin[] = {LO_AQ, LO_BQ, LO_CQ, LO_DQ};
int in_pin[] = {LI_A5, LI_B5, LI_C5, LI_D5};
int cur_y, i;
for (cur_y = 58; cur_y >= 55; cur_y--) {
for (i = 0; i < 4; i++) {
if (cur_y == 55 && i >= 2)
break;
fnet_new(&model, &net);
fnet_add_port(&model, net, cur_y, 13, DEV_LOGIC, DEV_LOG_M_OR_L, out_pin[i]);
fnet_add_port(&model, net, cur_y, 13, DEV_LOGIC, DEV_LOG_M_OR_L, in_pin[i]);
fnet_route(&model, net);
}
}
}
fnet_new(&model, &net);
fnet_add_port(&model, net, 55, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LO_CQ);
fnet_add_port(&model, net, 55, 13, DEV_LOGIC, DEV_LOG_M_OR_L, LI_C5);
fnet_add_port(&model, net, iob_led_y, iob_led_x, DEV_IOB,
iob_led_type_idx, IOB_IN_O);
fnet_route(&model, net);
write_floorplan(stdout, &model, FP_DEFAULT);
return fpga_free_model(&model);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL;
char *seqfile = NULL;
ESL_SQFILE *sqfp = NULL;
int infmt = eslSQFILE_UNKNOWN;
int alphatype = eslUNKNOWN;
ESL_ALPHABET *abc = NULL;
ESL_SQ *sq = NULL;
int64_t nseq = 0;
int64_t nres = 0;
int64_t small = 0;
int64_t large = 0;
double *monoc = NULL; /* monoresidue composition per sequence */
double *monoc_all = NULL; /* monoresidue composition over all seqs */
int do_comp = FALSE;
int status = eslOK;
int wstatus;
int i;
int x;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
seqfile = esl_opt_GetArg(go, 1);
do_comp = esl_opt_GetBoolean(go, "-c");
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_FormatCode(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat");
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file %s", seqfile);
else if (status == eslEFORMAT) esl_fatal("Format of seqfile %s unrecognized.", seqfile);
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
if (esl_opt_GetBoolean(go, "--rna")) alphatype = eslRNA;
else if (esl_opt_GetBoolean(go, "--dna")) alphatype = eslDNA;
else if (esl_opt_GetBoolean(go, "--amino")) alphatype = eslAMINO;
else {
status = esl_sqfile_GuessAlphabet(sqfp, &alphatype);
if (status == eslEAMBIGUOUS) esl_fatal("Couldn't guess alphabet from first sequence in %s", seqfile);
else if (status == eslEFORMAT) esl_fatal("Sequence file parse error, line %d of file %s:\n%s\n",
sqfp->linenumber, seqfile, sqfp->errbuf);
else if (status == eslENODATA) esl_fatal("Sequence file %s contains no data?", seqfile);
else if (status != eslOK) esl_fatal("Failed to guess alphabet (error code %d)\n", status);
}
abc = esl_alphabet_Create(alphatype);
sq = esl_sq_CreateDigital(abc);
esl_sqfile_SetDigital(sqfp, abc);
if (do_comp) {
ESL_ALLOC(monoc, (abc->Kp) * sizeof(double));
ESL_ALLOC(monoc_all, (abc->Kp) * sizeof(double));
esl_vec_DSet(monoc_all, abc->Kp, 0.0);
esl_vec_DSet(monoc, abc->Kp, 0.0);
}
while ((wstatus = esl_sqio_ReadWindow(sqfp, 0, 4096, sq)) != eslEOF)
{
if (wstatus == eslOK)
{
if (do_comp)
for (i = 1; i <= sq->n; i++)
monoc[sq->dsq[i]]++;
}
else if (wstatus == eslEOD)
{
if (nseq == 0) { small = large = sq->L; }
else {
small = ESL_MIN(small, sq->L);
large = ESL_MAX(large, sq->L);
}
if (esl_opt_GetBoolean(go, "-a")) {
printf("= %-20s %8" PRId64 " %s\n", sq->name, sq->L, (sq->desc != NULL) ? sq->desc : "");
}
nres += sq->L;
nseq++;
esl_sq_Reuse(sq);
if (do_comp) {
esl_vec_DAdd(monoc_all, monoc, abc->Kp);
esl_vec_DSet(monoc, abc->Kp, 0.0);
}
}
else if (wstatus == eslEFORMAT)
{
esl_fatal("Failed to parse sequence at line %ld, file %s:\n%s",
(long) sqfp->linenumber, sqfp->filename, sqfp->errbuf);
}
else
esl_fatal("Failed in reading sequence:\n%s\n", sqfp->errbuf);
}
printf("Format: %s\n", esl_sqio_DescribeFormat(sqfp->format));
printf("Alphabet type: %s\n", esl_abc_DescribeType(abc->type));
printf("Number of sequences: %" PRId64 "\n", nseq);
printf("Total # residues: %" PRId64 "\n", nres);
printf("Smallest: %" PRId64 "\n", small);
printf("Largest: %" PRId64 "\n", large);
printf("Average length: %.1f\n", (float) nres / (float) nseq);
if (do_comp) {
printf("\nResidue composition:\n");
for (x = 0; x < abc->Kp; x++)
if (x < abc->K || monoc_all[x] > 0)
printf("residue: %c %10.0f %.4f\n", abc->sym[x], monoc_all[x], monoc_all[x] / (double) nres);
free(monoc);
free(monoc_all);
}
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
return 0;
ERROR:
return status;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* command line configuration */
struct cfg_s cfg; /* application configuration */
char *basename= NULL; /* base of the output file names */
char *alifile = NULL; /* alignment file name */
char *dbfile = NULL; /* name of seq db file */
char outfile[256]; /* name of an output file */
int alifmt; /* format code for alifile */
int dbfmt; /* format code for dbfile */
ESLX_MSAFILE *afp = NULL; /* open alignment file */
ESL_MSA *origmsa = NULL; /* one multiple sequence alignment */
ESL_MSA *msa = NULL; /* MSA after frags are removed */
ESL_MSA *trainmsa= NULL; /* training set, aligned */
ESL_STACK *teststack=NULL; /* test set: stack of ESL_SQ ptrs */
int status; /* easel return code */
int nfrags; /* # of fragments removed */
int ntestdom; /* # of test domains */
int ntest; /* # of test sequences created */
int nali; /* number of alignments read */
double avgid;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h")) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 3) cmdline_failure(argv[0], "Incorrect number of command line arguments\n");
basename = esl_opt_GetArg(go, 1);
alifile = esl_opt_GetArg(go, 2);
dbfile = esl_opt_GetArg(go, 3);
alifmt = eslMSAFILE_STOCKHOLM;
dbfmt = eslSQFILE_FASTA;
/* Set up the configuration structure shared amongst functions here */
if (esl_opt_IsDefault(go, "--seed")) cfg.r = esl_randomness_CreateTimeseeded();
else cfg.r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
cfg.abc = NULL; /* until we open the MSA file, below */
cfg.fragfrac = esl_opt_GetReal(go, "-F");
cfg.idthresh1 = esl_opt_GetReal(go, "-1");
cfg.idthresh2 = esl_opt_GetReal(go, "-2");
cfg.test_lens = NULL;
cfg.ntest = 0;
cfg.max_ntest = (esl_opt_IsOn(go, "--maxtest") ? esl_opt_GetInteger(go, "--maxtest") : 0);
cfg.max_ntrain = (esl_opt_IsOn(go, "--maxtrain") ? esl_opt_GetInteger(go, "--maxtrain") : 0);
/* Open the output files */
if (snprintf(outfile, 256, "%s.msa", basename) >= 256) esl_fatal("Failed to construct output MSA file name");
if ((cfg.out_msafp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open MSA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.fa", basename) >= 256) esl_fatal("Failed to construct output FASTA file name");
if ((cfg.out_seqfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open FASTA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.pos", basename) >= 256) esl_fatal("Failed to construct pos test set summary file name");
if ((cfg.possummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.neg", basename) >= 256) esl_fatal("Failed to construct neg test set summary file name");
if ((cfg.negsummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open neg test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.tbl", basename) >= 256) esl_fatal("Failed to construct benchmark table file name");
if ((cfg.tblfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open benchmark table file %s\n", outfile);
if (esl_opt_GetBoolean(go, "--pid")) {
if (snprintf(outfile, 256, "%s.pid", basename) >= 256) esl_fatal("Failed to construct %%id table file name");
if ((cfg.pidfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open %%id table file %s\n", outfile);
} else cfg.pidfp = NULL;
/* Open the MSA file, digital mode; determine alphabet */
if (esl_opt_GetBoolean(go, "--amino")) cfg.abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) cfg.abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) cfg.abc = esl_alphabet_Create(eslRNA);
status = eslx_msafile_Open(&(cfg.abc), alifile, NULL, alifmt, NULL, &afp);
if (status != eslOK) eslx_msafile_OpenFailure(afp, status);
if (cfg.abc->type == eslAMINO) esl_composition_SW34(cfg.fq);
else esl_vec_DSet(cfg.fq, cfg.abc->K, 1.0 / (double) cfg.abc->K);
/* Open and process the dbfile; make sure it's in the same alphabet */
process_dbfile(&cfg, dbfile, dbfmt);
/* Read and process MSAs one at a time */
nali = 0;
while ((status = eslx_msafile_Read(afp, &origmsa)) != eslEOF)
{
if (status != eslOK) eslx_msafile_ReadFailure(afp, status);
esl_msa_ConvertDegen2X(origmsa);
esl_msa_Hash(origmsa);
remove_fragments(&cfg, origmsa, &msa, &nfrags);
separate_sets (&cfg, msa, &trainmsa, &teststack);
if ( esl_stack_ObjectCount(teststack) >= 2)
{
/* randomize test domain order, and apply size limit if any */
esl_stack_Shuffle(cfg.r, teststack);
if (cfg.max_ntest) pstack_select_topn(&teststack, cfg.max_ntest);
ntestdom = esl_stack_ObjectCount(teststack);
/* randomize training set alignment order, and apply size limit if any */
esl_msashuffle_PermuteSequenceOrder(cfg.r, trainmsa);
if (cfg.max_ntrain) msa_select_topn(&trainmsa, cfg.max_ntrain);
esl_msa_MinimGaps(trainmsa, NULL, NULL, FALSE);
if (esl_opt_GetBoolean(go, "--pid")) write_pids(cfg.pidfp, origmsa, trainmsa, teststack);
synthesize_positives(go, &cfg, msa->name, teststack, &ntest);
eslx_msafile_Write(cfg.out_msafp, trainmsa, eslMSAFILE_STOCKHOLM);
esl_dst_XAverageId(cfg.abc, trainmsa->ax, trainmsa->nseq, 10000, &avgid); /* 10000 is max_comparisons, before sampling kicks in */
fprintf(cfg.tblfp, "%-20s %3.0f%% %6d %6d %6d %6d %6d %6d\n", msa->name, 100.*avgid, (int) trainmsa->alen, msa->nseq, nfrags, trainmsa->nseq, ntestdom, ntest);
nali++;
}
esl_msa_Destroy(trainmsa);
esl_msa_Destroy(origmsa);
esl_msa_Destroy(msa);
}
if (nali == 0) esl_fatal("No alignments found in file %s\n", alifile);
synthesize_negatives(go, &cfg, esl_opt_GetInteger(go, "-N"));
fclose(cfg.out_msafp);
fclose(cfg.out_seqfp);
fclose(cfg.possummfp);
fclose(cfg.negsummfp);
fclose(cfg.tblfp);
if (cfg.pidfp) fclose(cfg.pidfp);
esl_randomness_Destroy(cfg.r);
esl_alphabet_Destroy(cfg.abc);
eslx_msafile_Close(afp);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *hmmfile = NULL; /* HMM file name */
char *seqfile = NULL; /* sequence file name */
char *mapfile = NULL; /* optional mapped MSA file name */
int infmt = eslSQFILE_UNKNOWN;
int outfmt = eslMSAFILE_STOCKHOLM;
P7_HMMFILE *hfp = NULL; /* open HMM file */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
char *outfile = NULL; /* output filename */
FILE *ofp = stdout; /* output stream */
ESL_SQ **sq = NULL; /* array of sequences */
void *p = NULL; /* tmp ptr for reallocation */
int nseq = 0; /* # of sequences in <seqfile> */
int mapseq = 0; /* # of sequences in mapped MSA */
int totseq = 0; /* # of seqs in all sources */
ESL_ALPHABET *abc = NULL; /* alphabet (set from the HMM file)*/
P7_HMM *hmm = NULL;
P7_TRACE **tr = NULL; /* array of tracebacks */
ESL_MSA *msa = NULL; /* resulting multiple alignment */
int msaopts = 0; /* flags to p7_tracealign_Seqs() */
int idx; /* counter over seqs, traces */
int status; /* easel/hmmer return code */
char errbuf[eslERRBUFSIZE];
/* Parse the command line
*/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
hmmfile = esl_opt_GetArg(go, 1);
seqfile = esl_opt_GetArg(go, 2);
if (strcmp(hmmfile, "-") == 0 && strcmp(seqfile, "-") == 0)
cmdline_failure(argv[0], "Either <hmmfile> or <seqfile> may be '-' (to read from stdin), but not both.\n");
msaopts |= p7_ALL_CONSENSUS_COLS; /* default as of 3.1 */
if (esl_opt_GetBoolean(go, "--trim")) msaopts |= p7_TRIM;
/* If caller declared an input format, decode it
*/
if (esl_opt_IsOn(go, "--informat")) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--informat"));
}
/* Determine output alignment file format */
outfmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat"));
if (outfmt == eslMSAFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a recognized output MSA file format\n", esl_opt_GetString(go, "--outformat"));
/* Open output stream */
if ( (outfile = esl_opt_GetString(go, "-o")) != NULL)
{
if ((ofp = fopen(outfile, "w")) == NULL)
cmdline_failure(argv[0], "failed to open -o output file %s for writing\n", outfile);
}
/* If caller forced an alphabet on us, create the one the caller wants
*/
if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA);
/* Read one HMM, and make sure there's only one.
*/
status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile, errbuf);
status = p7_hmmfile_Read(hfp, &abc, &hmm);
if (status == eslEFORMAT) p7_Fail("Bad file format in HMM file %s:\n%s\n", hfp->fname, hfp->errbuf);
else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
else if (status == eslEOF) p7_Fail("Empty HMM file %s? No HMM data found.\n", hfp->fname);
else if (status != eslOK) p7_Fail("Unexpected error in reading HMMs from %s\n", hfp->fname);
status = p7_hmmfile_Read(hfp, &abc, NULL);
if (status != eslEOF) p7_Fail("HMM file %s does not contain just one HMM\n", hfp->fname);
p7_hmmfile_Close(hfp);
/* We're going to build up two arrays: sequences and traces.
* If --mapali option is chosen, the first set of sequences/traces is from the provided alignment
*/
if ( (mapfile = esl_opt_GetString(go, "--mapali")) != NULL)
{
map_alignment(mapfile, hmm, &sq, &tr, &mapseq);
}
totseq = mapseq;
/* Read digital sequences into an array (possibly concat'ed onto mapped seqs)
*/
status = esl_sqfile_OpenDigital(abc, seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", seqfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", seqfile);
else if (status != eslOK) p7_Fail("Unexpected error %d opening sequence file %s\n", status, seqfile);
ESL_RALLOC(sq, p, sizeof(ESL_SQ *) * (totseq + 1));
sq[totseq] = esl_sq_CreateDigital(abc);
nseq = 0;
while ((status = esl_sqio_Read(sqfp, sq[totseq+nseq])) == eslOK)
{
nseq++;
ESL_RALLOC(sq, p, sizeof(ESL_SQ *) * (totseq+nseq+1));
sq[totseq+nseq] = esl_sq_CreateDigital(abc);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s", status, sqfp->filename);
esl_sqfile_Close(sqfp);
totseq += nseq;
/* Remaining initializations, including trace array allocation
*/
ESL_RALLOC(tr, p, sizeof(P7_TRACE *) * totseq);
for (idx = mapseq; idx < totseq; idx++)
tr[idx] = p7_trace_CreateWithPP();
p7_tracealign_computeTraces(hmm, sq, mapseq, totseq - mapseq, tr);
p7_tracealign_Seqs(sq, tr, totseq, hmm->M, msaopts, hmm, &msa);
eslx_msafile_Write(ofp, msa, outfmt);
for (idx = 0; idx <= totseq; idx++) esl_sq_Destroy(sq[idx]); /* including sq[nseq] because we overallocated */
for (idx = 0; idx < totseq; idx++) p7_trace_Destroy(tr[idx]);
free(sq);
free(tr);
esl_msa_Destroy(msa);
p7_hmm_Destroy(hmm);
if (ofp != stdout) fclose(ofp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return eslOK;
ERROR:
return status;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *hmmfile = NULL; /* HMM file name */
P7_HMMFILE *hfp = NULL; /* open HMM file */
FILE *ofp = NULL; /* output stream for HMMs */
int status; /* easel/hmmer return code */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) < 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the HMM file. */
hmmfile = esl_opt_GetArg(go, 1);
status = p7_hmmfile_Open(hmmfile, NULL, &hfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open HMM file %s for reading.\n", hmmfile);
else if (status == eslEFORMAT) p7_Fail("File %s does not appear to be in a recognized HMM format.\n", hmmfile);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n", status, hmmfile);
/* Open the output file, if any */
if (esl_opt_GetBoolean(go, "-O"))
{
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetArg(go, 2));
}
else if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Hand off to the appropriate routine */
if (esl_opt_GetBoolean(go, "--index"))
{
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
create_ssi_index(go, hfp);
}
else if (esl_opt_GetBoolean(go, "-f"))
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
multifetch(go, ofp, esl_opt_GetArg(go, 2), hfp);
}
else
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
onefetch(go, ofp, esl_opt_GetArg(go, 2), hfp);
if (ofp != stdout) printf("\n\nRetrieved HMM %s.\n", esl_opt_GetArg(go, 2));
}
if (esl_opt_GetBoolean(go, "-O") || esl_opt_GetString(go, "-o") != NULL) fclose(ofp);
p7_hmmfile_Close(hfp);
esl_getopts_Destroy(go);
exit(0);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *seqfile = NULL; /* sequence file name */
char *maskfile = NULL; /* mask coordinate file name */
int infmt = eslSQFILE_UNKNOWN; /* format code for seqfile */
int outfmt = eslSQFILE_FASTA; /* format code for output seqs */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
ESL_FILEPARSER *maskefp = NULL; /* open mask coord file */
FILE *ofp = NULL; /* output stream for masked seqs */
char *source = NULL; /* name of current seq to mask */
char *p1, *p2; /* pointers used in parsing */
int64_t start, end; /* start, end coord for masking */
int64_t i, j, pos; /* coords in a sequence */
int64_t overmask; /* # of extra residues to mask */
ESL_SQ *sq = esl_sq_Create(); /* current sequence */
int do_fetching;
int do_lowercase;
int maskchar;
int status; /* easel return code */
/****************************************************************************
* Parse command line
****************************************************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
do_fetching = esl_opt_GetBoolean(go, "-R");
do_lowercase = esl_opt_GetBoolean(go, "-l");
overmask = (esl_opt_IsOn(go, "-x") ? esl_opt_GetInteger(go, "-x") : 0);
maskchar = (esl_opt_IsOn(go, "-m") ? esl_opt_GetChar(go, "-m") : 'X');
seqfile = esl_opt_GetArg(go, 1);
maskfile = esl_opt_GetArg(go, 2);
/* Open the <seqfile>: text mode, not digital */
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a valid input sequence file format for --informat");
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n", seqfile);
else if (status == eslEFORMAT) cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
else if (status == eslEINVAL) cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
else if (status != eslOK) cmdline_failure(argv[0], "Open failed, code %d.\n", status);
if(do_fetching)
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
/* Open the <maskfile> */
if (esl_fileparser_Open(maskfile, NULL, &maskefp) != eslOK)
cmdline_failure(argv[0], "Failed to open mask coordinate file %s\n", maskfile);
esl_fileparser_SetCommentChar(maskefp, '#');
/* Open the output file, if any */
if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/****************************************************************************
* Main loop over lines in <maskfile>
****************************************************************************/
/* Read one data line at a time from the <maskfile>;
* parse into data fields <seqname> <start> <end>
*/
while (esl_fileparser_NextLine(maskefp) == eslOK)
{
/* First field is sequence name */
if (esl_fileparser_GetTokenOnLine(maskefp, &source, NULL) != eslOK)
esl_fatal("Failed to read source seq name on line %d of file %s\n", maskefp->linenumber, maskfile);
/* Get the sequence */
if (do_fetching)
{ /* If the <seqfile> is SSI indexed, try to reposition it and read <source> seq by random access */
status = esl_sqio_Fetch(sqfp, source, sq);
if (status == eslENOTFOUND) esl_fatal("seq %s not found in SSI index for file %s\n", source, sqfp->filename);
else if (status == eslEINVAL) esl_fatal("No SSI index or can't reposition in file %s\n", sqfp->filename);
else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected failure in fetching %s from file %s\n", source, sqfp->filename);
}
else
{ /* else, assume we're reading sequentially; <sqfile> and <maskfile> have seqs in same order */
status = esl_sqio_Read(sqfp, sq);
if (status == eslEOF) esl_fatal("File %s ended prematurely; didn't find %s\n", sqfp->filename, source);
else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected error reading sequence file %s\n", sqfp->filename);
if ((strcmp(sq->name, source) != 0) && (strcmp(sq->acc, source) != 0))
esl_fatal("Sequences in <sqfile> and <maskfile> aren't in same order; try -R");
}
/* If we're masking by lowercase, first make sure everything's uppercase */
if (do_lowercase)
for (pos = 0; pos < sq->n; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = toupper(sq->seq[pos]);
/* Next two fields are <start>, <end> for the masking */
/* possible future extension: wrap loop around this, enable multiple masked regions */
if (esl_fileparser_GetTokenOnLine(maskefp, &p1, NULL) != eslOK)
esl_fatal("Failed to read start coord on line %d of file %s\n", maskefp->linenumber, maskfile);
start = strtoll(p1, &p2, 0) - 1;
if (esl_fileparser_GetTokenOnLine(maskefp, &p2, NULL) != eslOK)
esl_fatal("Failed to read end coord on line %d of file %s\n", maskefp->linenumber, maskfile);
end = strtoll(p2, &p1, 0) - 1;
/* Do the masking */
if (esl_opt_GetBoolean(go, "-r")) /* Reverse masking */
{ /* leave start..end unmasked; mask prefix 0..start-1, end+1..L-1 */
i = 0;
j = ESL_MIN(sq->n-1, start - 1 + overmask);
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
i = ESL_MAX(0, end + 1 - overmask);
j = sq->n-1;
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
}
else
{ /* normal: mask start..end */
i = ESL_MAX(0, start - overmask);
j = ESL_MIN(sq->n-1, end + overmask);
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
}
esl_sqio_Write(ofp, sq, outfmt, FALSE);
esl_sq_Reuse(sq);
}
esl_sq_Destroy(sq);
esl_fileparser_Close(maskefp);
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
if (ofp != stdout) fclose(ofp);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *alifile = NULL; /* alignment file name */
int infmt = eslMSAFILE_UNKNOWN; /* format code for alifile */
int outfmt = eslMSAFILE_UNKNOWN; /* output format for fetched msa's */
ESLX_MSAFILE *afp = NULL; /* open alignment file */
FILE *ofp = NULL; /* output stream for alignments */
int status; /* easel return code */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) < 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
if (esl_opt_IsOn(go, "--informat")) {
infmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslMSAFILE_UNKNOWN) esl_fatal("%s is not a valid input alignment file format for --informat", esl_opt_GetString(go, "--informat"));
}
outfmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat"));
if (outfmt == eslMSAFILE_UNKNOWN) esl_fatal("%s is not a valid output alignment file format for --outformat", esl_opt_GetString(go, "--outformat"));
alifile = esl_opt_GetArg(go, 1);
/* Open the alignment file. */
if ( (status = eslx_msafile_Open(NULL, alifile, NULL, infmt, NULL, &afp)) != eslOK)
eslx_msafile_OpenFailure(afp, status);
/* Open the SSI index, if any */
if (! esl_opt_GetBoolean(go, "--index"))
{
if (afp->bf->mode_is == eslBUFFER_FILE ||
afp->bf->mode_is == eslBUFFER_ALLFILE ||
afp->bf->mode_is == eslBUFFER_MMAP)
{
char *ssifile = NULL;
esl_sprintf(&ssifile, "%s.ssi", afp->bf->filename);
status = esl_ssi_Open(ssifile, &(afp->ssi));
if (status == eslERANGE ) esl_fatal("SSI index %s has 64-bit offsets; this system doesn't support them", ssifile);
else if (status == eslEFORMAT) esl_fatal("SSI index %s has an unrecognized format. Try recreating, w/ esl-afetch --index", ssifile);
else if (status == eslENOTFOUND) afp->ssi = NULL;
else if (status != eslOK) esl_fatal("SSI index %s: open failed, error code %d\n", ssifile, status);
free(ssifile);
}
}
/* Open the output file, if any
*/
if (esl_opt_GetBoolean(go, "-O"))
{
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetArg(go, 2));
}
else if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Hand off control flow as appropriate */
if (esl_opt_GetBoolean(go, "--index"))
{
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
create_ssi_index(go, afp);
}
else if (esl_opt_GetBoolean(go, "-f"))
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
multifetch(go, ofp, outfmt, esl_opt_GetArg(go, 2), afp);
}
else
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
onefetch(go, ofp, outfmt, esl_opt_GetArg(go, 2), afp);
if (ofp != stdout) printf("\n\nRetrieved alignment %s.\n", esl_opt_GetArg(go, 2));
}
eslx_msafile_Close(afp);
esl_getopts_Destroy(go);
exit(0);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *seqfile = NULL; /* sequence file name */
int infmt = eslSQFILE_UNKNOWN; /* format code for seqfile */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
FILE *ofp = NULL; /* output stream for sequences */
int status; /* easel return code */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) < 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the sequence file */
seqfile = esl_opt_GetArg(go, 1);
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat", esl_opt_GetString(go, "--informat"));
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n", seqfile);
else if (status == eslEFORMAT) cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
else if (status == eslEINVAL) cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
else if (status != eslOK) cmdline_failure(argv[0], "Open failed, code %d.\n", status);
/* Open the output file, if any */
if (esl_opt_GetBoolean(go, "-O"))
{
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetArg(go, 2));
}
else if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Indexing mode */
if (esl_opt_GetBoolean(go, "--index"))
{
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
if (sqfp->data.ascii.do_gzip) cmdline_failure(argv[0], "Can't index a .gz compressed file");
if (sqfp->data.ascii.do_stdin) cmdline_failure(argv[0], "Can't index a standard input pipe");
create_ssi_index(go, sqfp);
}
/* List retrieval mode */
else if (esl_opt_GetBoolean(go, "-f"))
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the SSI index for retrieval */
if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->format))
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
if (esl_opt_GetBoolean(go, "-C")) multifetch_subseq(go, ofp, esl_opt_GetArg(go, 2), sqfp);
else multifetch (go, ofp, esl_opt_GetArg(go, 2), sqfp);
}
/* Single sequence retrieval mode */
else
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
char *key = esl_opt_GetArg(go, 2);
char *cstring = esl_opt_GetString(go, "-c");
char *newname = esl_opt_GetString(go, "-n");
/* Open the SSI index for retrieval */
if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->format))
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
/* -c: subsequence retrieval; else full sequence retrieval */
if (cstring != NULL)
{
uint32_t start, end;
status = esl_regexp_ParseCoordString(cstring, &start, &end);
if (status == eslESYNTAX) esl_fatal("-c takes arg of subseq coords <from>..<to>; %s not recognized", cstring);
if (status == eslFAIL) esl_fatal("Failed to find <from> or <to> coord in %s", cstring);
onefetch_subseq(go, ofp, sqfp, newname, key, start, end);
if (ofp != stdout) printf("\n\nRetrieved subsequence %s/%d-%d.\n", key, start, end);
}
else
{
onefetch(go, ofp, esl_opt_GetArg(go, 2), sqfp);
if (ofp != stdout) printf("\n\nRetrieved sequence %s.\n", esl_opt_GetArg(go, 2));
}
}
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* command line configuration */
struct cfg_s cfg; /* application configuration */
char *basename= NULL; /* base of the output file names */
char *alifile = NULL; /* alignment file name */
char *dbfile = NULL; /* name of seq db file */
char outfile[256]; /* name of an output file */
int alifmt; /* format code for alifile */
int dbfmt; /* format code for dbfile */
ESL_MSAFILE *afp = NULL; /* open alignment file */
ESL_MSA *origmsa = NULL; /* one multiple sequence alignment */
ESL_MSA *msa = NULL; /* MSA after frags are removed */
ESL_MSA *trainmsa= NULL; /* training set, aligned */
ESL_STACK *teststack=NULL; /* test set: stack of ESL_SQ ptrs */
int status; /* easel return code */
int nfrags; /* # of fragments removed */
int ntestdom; /* # of test domains */
int ntest; /* # of test sequences created */
int nali; /* number of alignments read */
double avgid;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h")) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 3) cmdline_failure(argv[0], "Incorrect number of command line arguments\n");
basename = esl_opt_GetArg(go, 1);
alifile = esl_opt_GetArg(go, 2);
dbfile = esl_opt_GetArg(go, 3);
alifmt = eslMSAFILE_STOCKHOLM;
dbfmt = eslSQFILE_FASTA;
/* Set up the configuration structure shared amongst functions here */
if (esl_opt_IsDefault(go, "--seed")) cfg.r = esl_randomness_CreateTimeseeded();
else cfg.r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
cfg.abc = NULL; /* until we open the MSA file, below */
cfg.fragfrac = esl_opt_GetReal(go, "-F");
cfg.idthresh1 = esl_opt_GetReal(go, "-1");
cfg.idthresh2 = esl_opt_GetReal(go, "-2");
cfg.test_lens = NULL;
cfg.ntest = 0;
/* Open the output files */
if (snprintf(outfile, 256, "%s.msa", basename) >= 256) esl_fatal("Failed to construct output MSA file name");
if ((cfg.out_msafp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open MSA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.fa", basename) >= 256) esl_fatal("Failed to construct output FASTA file name");
if ((cfg.out_seqfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open FASTA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.pos", basename) >= 256) esl_fatal("Failed to construct pos test set summary file name");
if ((cfg.possummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.neg", basename) >= 256) esl_fatal("Failed to construct neg test set summary file name");
if ((cfg.negsummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open neg test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.tbl", basename) >= 256) esl_fatal("Failed to construct benchmark table file name");
if ((cfg.tblfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open benchmark table file %s\n", outfile);
/* Open the MSA file; determine alphabet */
status = esl_msafile_Open(alifile, alifmt, NULL, &afp);
if (status == eslENOTFOUND) esl_fatal("Alignment file %s doesn't exist or is not readable\n", alifile);
else if (status == eslEFORMAT) esl_fatal("Couldn't determine format of alignment %s\n", alifile);
else if (status != eslOK) esl_fatal("Alignment file open failed with error %d\n", status);
if (esl_opt_GetBoolean(go, "--amino")) cfg.abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) cfg.abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) cfg.abc = esl_alphabet_Create(eslRNA);
else {
int type;
status = esl_msafile_GuessAlphabet(afp, &type);
if (status == eslEAMBIGUOUS) esl_fatal("Failed to guess the bio alphabet used in %s.\nUse --dna, --rna, or --amino option to specify it.", alifile);
else if (status == eslEFORMAT) esl_fatal("Alignment file parse failed: %s\n", afp->errbuf);
else if (status == eslENODATA) esl_fatal("Alignment file %s is empty\n", alifile);
else if (status != eslOK) esl_fatal("Failed to read alignment file %s\n", alifile);
cfg.abc = esl_alphabet_Create(type);
}
esl_msafile_SetDigital(afp, cfg.abc);
if (cfg.abc->type == eslAMINO) esl_composition_SW34(cfg.fq);
else esl_vec_DSet(cfg.fq, cfg.abc->K, 1.0 / (double) cfg.abc->K);
/* Open and process the dbfile; make sure it's in the same alphabet */
process_dbfile(&cfg, dbfile, dbfmt);
/* Read and process MSAs one at a time */
nali = 0;
while ((status = esl_msa_Read(afp, &origmsa)) == eslOK)
{
remove_fragments(&cfg, origmsa, &msa, &nfrags);
separate_sets (&cfg, msa, &trainmsa, &teststack);
ntestdom = esl_stack_ObjectCount(teststack);
if (ntestdom >= 2)
{
esl_stack_Shuffle(cfg.r, teststack);
synthesize_positives(go, &cfg, msa->name, teststack, &ntest);
esl_msa_MinimGaps(trainmsa, NULL, NULL);
esl_msa_Write(cfg.out_msafp, trainmsa, eslMSAFILE_STOCKHOLM);
esl_dst_XAverageId(cfg.abc, trainmsa->ax, trainmsa->nseq, 10000, &avgid); /* 10000 is max_comparisons, before sampling kicks in */
fprintf(cfg.tblfp, "%-20s %3.0f%% %6d %6d %6d %6d %6d %6d\n", msa->name, 100.*avgid, (int) trainmsa->alen, msa->nseq, nfrags, trainmsa->nseq, ntestdom, ntest);
nali++;
}
esl_msa_Destroy(trainmsa);
esl_msa_Destroy(origmsa);
esl_msa_Destroy(msa);
}
if (status == eslEFORMAT) esl_fatal("Alignment file parse error, line %d of file %s:\n%s\nOffending line is:\n%s\n",
afp->linenumber, afp->fname, afp->errbuf, afp->buf);
else if (status != eslEOF) esl_fatal("Alignment file read failed with error code %d\n", status);
else if (nali == 0) esl_fatal("No alignments found in file %s\n", alifile);
if (nali > 0)
synthesize_negatives(go, &cfg, esl_opt_GetInteger(go, "-N"));
fclose(cfg.out_msafp);
fclose(cfg.out_seqfp);
fclose(cfg.possummfp);
fclose(cfg.negsummfp);
fclose(cfg.tblfp);
esl_randomness_Destroy(cfg.r);
esl_alphabet_Destroy(cfg.abc);
esl_msafile_Close(afp);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL;
ESL_RANDOMNESS *r = NULL;
int nselect = 0;
char *filename = NULL;
FILE *fp = NULL;
char **larr = NULL;
char *buf = NULL;
int buflen = 0;
char *tmp = NULL;
int i,j;
int n;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
nselect = atoi(esl_opt_GetArg(go, 1));
filename = esl_opt_GetArg(go, 2);
r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
if ((larr = malloc(sizeof(char *) * nselect)) == NULL) esl_fatal("allocation failed");
if (strcmp(filename, "-") == 0) fp = stdin;
else {
if ((fp = fopen(filename, "r")) == NULL) esl_fatal("Failed to open file %s\n", filename);
}
n = 0;
while (esl_fgets(&buf, &buflen, fp) == eslOK)
{
n++;
i = esl_rnd_Roll(r, n);
if (i < nselect) {
for (j = i; j < nselect && j < n; j++)
{
tmp = larr[j];
larr[j] = buf;
buf = tmp;
}
free(buf);
buf = NULL;
buflen = 0;
}
}
for (i = 0; i < nselect; i++) printf("%s", larr[i]);
if (fp != stdin) fclose(fp);
for (i = 0; i < nselect; i++) free(larr[i]);
free(larr);
free(buf);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
ESL_RANDOMNESS *r = NULL; /* source of randomness */
char *hmmfile = NULL; /* file to read HMM(s) from */
P7_HMMFILE *hfp = NULL; /* open hmmfile */
P7_HMM *hmm = NULL; /* HMM to emit from */
FILE *ofp = NULL; /* output stream */
int outfmt = 0;
int nhmms = 0;
int status;
char errbuf[eslERRBUFSIZE];
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h")) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
if ((hmmfile = esl_opt_GetArg(go, 1)) == NULL) cmdline_failure(argv[0], "Failed to get <hmmfile> on cmdline: %s\n", go->errbuf);
if ( esl_opt_IsOn(go, "-o") ) {
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s", esl_opt_GetString(go, "-o"));
} else ofp = stdout;
if (esl_opt_GetBoolean(go, "-a")) outfmt = eslMSAFILE_STOCKHOLM;
else outfmt = eslSQFILE_FASTA;
r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "--seed"));
status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile, errbuf);
while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
{
if (status == eslEFORMAT) esl_fatal("Bad file format in HMM file %s:\n%s\n", hfp->fname, hfp->errbuf);
else if (status == eslEINCOMPAT) esl_fatal("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
else if (status != eslOK) esl_fatal("Unexpected error in reading HMMs from %s\n", hfp->fname);
nhmms++;
if (esl_opt_GetBoolean(go, "-c")) emit_consensus(go, ofp, outfmt, hmm);
else if (esl_opt_GetBoolean(go, "-C")) emit_fancycons(go, ofp, outfmt, hmm);
else if (esl_opt_GetBoolean(go, "-a")) emit_alignment(go, ofp, outfmt, r, hmm);
else emit_sequences(go, ofp, outfmt, r, hmm);
p7_hmm_Destroy(hmm);
}
if (nhmms == 0) esl_fatal("Empty HMM file %s? No HMM data found.\n");
if (esl_opt_IsOn(go, "-o")) { fclose(ofp); }
esl_randomness_Destroy(r);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
p7_hmmfile_Close(hfp);
return eslOK;
}
