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; /* 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; /* application configuration */
ESL_ALPHABET *abc = NULL; /* biological alphabet */
char *alifile = NULL; /* alignment file name */
int fmt = eslMSAFILE_UNKNOWN; /* format code for alifile */
ESLX_MSAFILE *afp = NULL; /* open msa file */
ESL_MSAFILE2 *old_afp = NULL; /* open msa file, legacy (--small) */
ESL_MSA *msa = NULL; /* one multiple sequence alignment */
int nali; /* number of alignments read */
int i; /* counter over seqs */
int64_t alen; /* alignment length */
int nseq; /* number of sequences in the msa */
int64_t rlen; /* a raw (unaligned) seq length */
int64_t small, large; /* smallest, largest sequence */
int64_t nres; /* total # of residues in msa */
double avgid; /* average fractional pair id */
int max_comparisons; /* maximum # comparisons for avg id */
int do_stall; /* used to stall when debugging */
double **abc_ct = NULL; /* [0..msa->alen-1][0..abc->K] number of each residue at each position (abc->K is gap) */
double ***bp_ct = NULL; /* [0..msa->alen-1][0..abc->Kp-1][0..abc->Kp-1] per (non-pknotted) consensus basepair *
* count of each possible basepair over all seqs basepairs are indexed by 'i' the minimum *
* of 'i:j' for a pair between i and j, where i < j. */
double **pp_ct = NULL; /* [0..msa->alen-1][0..11], count of each posterior probability (PP) code, over all sequences, gap is 11 */
int *i_am_rf = NULL; /* [0..i..msa->alen-1]: TRUE if pos i is non-gap RF posn, if msa->rf == NULL remains NULL */
int *rf2a_map = NULL; /* [0..rfpos..rflen-1] = apos,
* apos is the alignment position (0..msa->alen-1) that
* is non-gap RF position rfpos+1 (for rfpos in 0..rflen-1) */
int rflen = -1; /* nongap RF length */
char errbuf[eslERRBUFSIZE];
int status; /* easel return code */
/* optional output files */
FILE *iinfofp = NULL; /* output file for --iinfo */
FILE *pcinfofp = NULL; /* output file for --pcinfo */
FILE *psinfofp = NULL; /* output file for --psinfo */
FILE *rinfofp = NULL; /* output file for --rinfo */
FILE *icinfofp = NULL; /* output file for --icinfo */
FILE *listfp = NULL; /* output file for --list */
FILE *cinfofp = NULL; /* output file for --cinfo */
FILE *bpinfofp = NULL; /* output file for --bpinfo */
int use_weights; /* TRUE if --weight, reported weighted counts (using msa->wgt) to all output files */
int weights_exist; /* TRUE if at least one msa->wgt value differs from 1.0, FALSE if not (or if msa->wgt==NULL) */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK ||
esl_opt_VerifyConfig(go) != eslOK)
{
printf("Failed to parse command line: %s\n", go->errbuf);
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if (esl_opt_GetBoolean(go, "-h") )
{
esl_banner(stdout, argv[0], banner);
esl_usage (stdout, argv[0], usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
puts("\n small memory mode, requires --amino,--dna, or --rna and --informat pfam:");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
puts("\n optional output files:");
esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
exit(0);
}
if (esl_opt_ArgNumber(go) != 1)
{
printf("Incorrect number of command line arguments.\n");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
alifile = esl_opt_GetArg(go, 1);
if (esl_opt_IsOn(go, "--informat") &&
(fmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"))) == eslMSAFILE_UNKNOWN)
esl_fatal("%s is not a valid input sequence file format for --informat", esl_opt_GetString(go, "--informat"));
if (esl_opt_GetBoolean(go, "--small") && fmt != eslMSAFILE_PFAM) esl_fatal("--small requires --informat pfam\n");
max_comparisons = 1000;
do_stall = esl_opt_GetBoolean(go, "--stall"); /* a stall point for attaching gdb */
while (do_stall);
/***********************************************
* Open the MSA file; determine alphabet; set for digital input
***********************************************/
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);
/* We'd like to get rid of the legacy msafile interface, but it
* includes small memory functionality for Pfam format which we have
* to replace first. For now, use both interfaces, new and legacy
*/
if ( esl_opt_GetBoolean(go, "--small") )
{
if (! abc) esl_fatal("--small requires one of --amino, --dna, --rna be specified.");
status = esl_msafile2_OpenDigital(abc, alifile, NULL, &old_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);
}
else
{
if ( (status = eslx_msafile_Open(&abc, alifile, NULL, fmt, NULL, &afp)) != eslOK)
eslx_msafile_OpenFailure(afp, status);
}
/**************************************
* Open optional output files, as nec *
**************************************/
/* determine name for first list file, if nec */
if( esl_opt_IsOn(go, "--list")) {
if ((listfp = fopen(esl_opt_GetString(go, "--list"), "w")) == NULL)
esl_fatal("Failed to open --list output file %s\n", esl_opt_GetString(go, "--list"));
}
if( esl_opt_IsOn(go, "--icinfo")) {
if ((icinfofp = fopen(esl_opt_GetString(go, "--icinfo"), "w")) == NULL)
esl_fatal("Failed to open --icinfo output file %s\n", esl_opt_GetString(go, "--icinfo"));
}
if( esl_opt_IsOn(go, "--rinfo")) {
if ((rinfofp = fopen(esl_opt_GetString(go, "--rinfo"), "w")) == NULL)
esl_fatal("Failed to open --rinfo output file %s\n", esl_opt_GetString(go, "--rinfo"));
}
if( esl_opt_IsOn(go, "--pcinfo")) {
if ((pcinfofp = fopen(esl_opt_GetString(go, "--pcinfo"), "w")) == NULL)
esl_fatal("Failed to open --pcinfo output file %s\n", esl_opt_GetString(go, "--pcinfo"));
}
if( esl_opt_IsOn(go, "--psinfo")) {
if ((psinfofp = fopen(esl_opt_GetString(go, "--psinfo"), "w")) == NULL)
esl_fatal("Failed to open --psinfo output file %s\n", esl_opt_GetString(go, "--psinfo"));
}
if( esl_opt_IsOn(go, "--iinfo")) {
if ((iinfofp = fopen(esl_opt_GetString(go, "--iinfo"), "w")) == NULL)
esl_fatal("Failed to open --iinfo output file %s\n", esl_opt_GetString(go, "--iinfo"));
}
if( esl_opt_IsOn(go, "--cinfo")) {
if ((cinfofp = fopen(esl_opt_GetString(go, "--cinfo"), "w")) == NULL)
esl_fatal("Failed to open --cinfo output file %s\n", esl_opt_GetString(go, "--cinfo"));
}
if( esl_opt_IsOn(go, "--bpinfo")) {
if ((bpinfofp = fopen(esl_opt_GetString(go, "--bpinfo"), "w")) == NULL)
esl_fatal("Failed to open --bpinfo output file %s\n", esl_opt_GetString(go, "--bpinfo"));
}
/***********************************************
* Read MSAs one at a time.
***********************************************/
if (esl_opt_GetBoolean(go, "-1")) {
puts("#");
if(! esl_opt_GetBoolean(go, "--small")) {
printf("# %-4s %-20s %10s %7s %7s %12s %6s %6s %10s %3s\n", "idx", "name", "format", "nseq", "alen", "nres", "small", "large", "avlen", "%id");
printf("# %-4s %-20s %10s %7s %7s %12s %6s %6s %10s %3s\n", "----", "--------------------", "----------", "-------", "-------", "------------", "------", "------", "----------", "---");
}
else {
printf("# %-4s %-20s %10s %7s %7s %12s %10s\n", "idx", "name", "format", "nseq", "alen", "nres", "avlen");
printf("# %-4s %-20s %10s %7s %7s %12s %10s\n", "----", "--------------------", "----------", "-------", "-------", "------------", "----------");
}
}
nali = 0;
fmt = (esl_opt_GetBoolean(go, "--small") ? old_afp->format : afp->format);
while ( (status = ( esl_opt_GetBoolean(go, "--small") ?
esl_msafile2_ReadInfoPfam(old_afp, listfp, abc, -1, NULL, NULL, &msa, &nseq, &alen, NULL, NULL, NULL, NULL, NULL, &abc_ct, &pp_ct, NULL, NULL, NULL) :
eslx_msafile_Read (afp, &msa))) == eslOK)
{
nali++;
nres = 0;
if (! esl_opt_GetBoolean(go, "--small")) {
nseq = msa->nseq;
alen = msa->alen;
small = large = -1;
for (i = 0; i < msa->nseq; i++)
{
rlen = esl_abc_dsqrlen(msa->abc, msa->ax[i]);
nres += rlen;
if (small == -1 || rlen < small) small = rlen;
if (large == -1 || rlen > large) large = rlen;
}
esl_dst_XAverageId(abc, msa->ax, msa->nseq, max_comparisons, &avgid);
}
else { /* --small invoked */
for(i = 0; i < alen; i++) nres += (int) esl_vec_DSum(abc_ct[i], abc->K);
}
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-6d %-20s %10s %7d %7" PRId64 " %12" PRId64,
nali,
msa->name,
eslx_msafile_DecodeFormat(fmt),
nseq,
alen,
nres);
if (! esl_opt_GetBoolean(go, "--small")) {
printf(" %6" PRId64 " %6" PRId64 " %10.1f %3.0f\n",
small,
large,
(double) nres / (double) msa->nseq,
100.*avgid);
}
else {
printf(" %10.1f\n", (double) nres / (double) nseq);
}
}
else
{
printf("Alignment number: %d\n", nali);
if (msa->name != NULL)
printf("Alignment name: %s\n", msa->name);
printf("Format: %s\n", eslx_msafile_DecodeFormat(fmt));
printf("Number of sequences: %d\n", nseq);
printf("Alignment length: %" PRId64 "\n", alen);
printf("Total # residues: %" PRId64 "\n", nres);
if(! esl_opt_GetBoolean(go, "--small")) {
printf("Smallest: %" PRId64 "\n", small);
printf("Largest: %" PRId64 "\n", large);
}
printf("Average length: %.1f\n", (double) nres / (double) nseq);
if(! esl_opt_GetBoolean(go, "--small")) {
printf("Average identity: %.0f%%\n", 100.*avgid);
}
printf("//\n");
}
/* Dump data to optional output files, if nec */
if(esl_opt_IsOn(go, "--list")) {
if(! esl_opt_GetBoolean(go, "--small")) {
/* only print sequence name to list file if ! --small, else we already have in esl_msafile2_ReadInfoPfam() */
for(i = 0; i < msa->nseq; i++) fprintf(listfp, "%s\n", msa->sqname[i]);
}
}
/* if RF exists, get i_am_rf array[0..alen] which tells us which positions are non-gap RF positions
* and rf2a_map, a map of non-gap RF positions to overall alignment positions */
if(msa->rf != NULL) {
if((status = map_rfpos_to_apos(msa, abc, errbuf, alen, &i_am_rf, &rf2a_map, &rflen)) != eslOK) esl_fatal(errbuf);
}
else i_am_rf = NULL;
weights_exist = check_msa_weights(msa);
use_weights = (weights_exist && esl_opt_GetBoolean(go, "--weight")) ? TRUE : FALSE;
if( (! esl_opt_GetBoolean(go, "--small")) &&
(esl_opt_IsOn(go, "--icinfo") || esl_opt_IsOn(go, "--rinfo") || esl_opt_IsOn(go, "--pcinfo") ||
esl_opt_IsOn(go, "--cinfo") || esl_opt_IsOn(go, "--bpinfo"))) {
/* collect counts of each residue and PPs (if they exist) from the msa */
if(esl_opt_GetBoolean(go, "--weight") && msa->wgt == NULL) esl_fatal("--weight requires all alignments have #=GS WT annotation, but aln %d does not", nali);
if((status = count_msa(msa, errbuf, nali,
esl_opt_GetBoolean(go, "--noambig"), /* ignore ambiguous residues? */
esl_opt_GetBoolean(go, "--weight"), /* use msa->wgt sequence weights? */
&abc_ct,
((bpinfofp != NULL && msa->ss_cons != NULL) ? &bp_ct : NULL), /* get basepair counts? */
(msa->pp != NULL ? &pp_ct : NULL))) /* get PP counts? */
!= eslOK) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--icinfo")) {
if((status = dump_infocontent_info(icinfofp, abc, abc_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--rinfo")) {
if((status = dump_residue_info(rinfofp, abc, abc_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if(esl_opt_IsOn(go, "--pcinfo")) {
if(pp_ct == NULL) esl_fatal("Error: --pcinfo requires all alignments have #=GR PP annotation, but alignment %d does not", nali);
if((status = dump_posterior_column_info(pcinfofp, pp_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if(esl_opt_IsOn(go, "--psinfo")) {
if(msa->pp == NULL) esl_fatal("Error: --psinfo requires all alignments have #=GR PP annotation, but alignment %d does not", nali);
if((status = dump_posterior_sequence_info(psinfofp, msa, nali, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--iinfo")) {
if(msa->rf == NULL) esl_fatal("--iinfo requires all alignments have #=GC RF annotation, but alignment %d does not", nali);
if(esl_opt_GetBoolean(go, "--weight") && msa->wgt == NULL) esl_fatal("--weight requires all alignments have #=GS WT annotation, but aln %d does not", nali);
if((status = dump_insert_info(iinfofp, msa, use_weights, nali, i_am_rf, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--cinfo")) {
if((status = dump_column_residue_counts(cinfofp, abc, abc_ct, esl_opt_GetBoolean(go, "--noambig"), use_weights, nali, alen, nseq, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--bpinfo")) {
if(msa->ss_cons == NULL) esl_fatal("--bpinfo requires all alignments have #=GC SS_cons annotation, but alignment %d does not", nali);
if((status = dump_basepair_counts(bpinfofp, msa, abc, bp_ct, use_weights, nali, nseq, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
esl_msa_Destroy(msa);
if(abc_ct != NULL) { esl_Free2D((void **) abc_ct, alen); abc_ct = NULL; }
if(bp_ct != NULL) { esl_Free3D((void ***) bp_ct, alen, abc->Kp); bp_ct = NULL; }
if(pp_ct != NULL) { esl_Free2D((void **) pp_ct, alen); pp_ct = NULL; }
if(i_am_rf != NULL) { free(i_am_rf); i_am_rf = NULL; }
if(rf2a_map != NULL) { free(rf2a_map); rf2a_map = NULL; }
}
/* If an msa read failed, we've dropped out to here with an informative status code.
* we have to handle failures from new vs. legacy msa parsing differently
*/
if (esl_opt_GetBoolean(go, "--small"))
{
if (status == eslEFORMAT) esl_fatal("Alignment file parse error, line %d of file %s:\n%s\nOffending line is:\n%s\n", old_afp->linenumber, old_afp->fname, old_afp->errbuf, old_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);
}
else
{
if (nali == 0 || status != eslEOF) eslx_msafile_ReadFailure(afp, status);
}
/* Cleanup, normal return
*/
if(listfp != NULL) {
fclose(listfp);
printf("# List of sequences in %d alignment(s) saved to file %s\n", nali, esl_opt_GetString(go, "--list"));
}
if(icinfofp != NULL) {
fclose(icinfofp);
printf("# Information content data saved to file %s.\n", esl_opt_GetString(go, "--icinfo"));
}
if(rinfofp != NULL) {
fclose(rinfofp);
printf("# Residue data saved to file %s.\n", esl_opt_GetString(go, "--rinfo"));
}
if(pcinfofp != NULL) {
fclose(pcinfofp);
printf("# Per-column posterior probability data saved to file %s.\n", esl_opt_GetString(go, "--pcinfo"));
}
if(psinfofp != NULL) {
fclose(psinfofp);
printf("# Per-sequence posterior probability data saved to file %s.\n", esl_opt_GetString(go, "--psinfo"));
}
if(iinfofp != NULL) {
printf("# Insert data saved to file %s.\n", esl_opt_GetString(go, "--iinfo"));
fclose(iinfofp);
}
if(cinfofp != NULL) {
printf("# Per-column counts data saved to file %s.\n", esl_opt_GetString(go, "--cinfo"));
fclose(cinfofp);
}
if(bpinfofp != NULL) {
printf("# Per-column basepair counts data saved to file %s.\n", esl_opt_GetString(go, "--bpinfo"));
fclose(bpinfofp);
}
if (afp) eslx_msafile_Close(afp);
if (old_afp) esl_msafile2_Close(old_afp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
