static void
utest_goodfile(char *filename, int testnumber, int expected_alphatype, int expected_nseq, int expected_alen)
{
ESL_ALPHABET *abc = NULL;
ESLX_MSAFILE *afp = NULL;
ESL_MSA *msa1 = NULL;
ESL_MSA *msa2 = NULL;
char tmpfile1[32] = "esltmpXXXXXX";
char tmpfile2[32] = "esltmpXXXXXX";
FILE *ofp = NULL;
int status;
/* guessing both the format and the alphabet should work: this is a digital open */
/* PSIBLAST format is autodetected as SELEX, which is fine - selex parser is more general */
if ( (status = eslx_msafile_Open(&abc, filename, NULL, eslMSAFILE_UNKNOWN, NULL, &afp)) != eslOK) esl_fatal("psiblast good file test %d failed: digital open", testnumber);
if (afp->format != eslMSAFILE_SELEX) esl_fatal("psiblast good file test %d failed: format autodetection", testnumber);
if (abc->type != expected_alphatype) esl_fatal("psiblast good file test %d failed: alphabet autodetection", testnumber);
afp->format = eslMSAFILE_PSIBLAST;
/* This is a digital read, using <abc>. */
if ( (status = esl_msafile_psiblast_Read(afp, &msa1)) != eslOK) esl_fatal("psiblast good file test %d failed: msa read, digital", testnumber);
if (msa1->nseq != expected_nseq || msa1->alen != expected_alen) esl_fatal("psiblast good file test %d failed: nseq/alen", testnumber);
if (esl_msa_Validate(msa1, NULL) != eslOK) esl_fatal("psiblast good file test %d failed: msa1 invalid", testnumber);
eslx_msafile_Close(afp);
/* write it back out to a new tmpfile (digital write) */
if ( (status = esl_tmpfile_named(tmpfile1, &ofp)) != eslOK) esl_fatal("psiblast good file test %d failed: tmpfile creation", testnumber);
if ( (status = esl_msafile_psiblast_Write(ofp, msa1)) != eslOK) esl_fatal("psiblast good file test %d failed: msa write, digital", testnumber);
fclose(ofp);
/* now open and read it as text mode, in known format. (We have to pass fmtd now, to deal with the possibility of a nonstandard name width) */
if ( (status = eslx_msafile_Open(NULL, tmpfile1, NULL, eslMSAFILE_PSIBLAST, NULL, &afp)) != eslOK) esl_fatal("psiblast good file test %d failed: text mode open", testnumber);
if ( (status = esl_msafile_psiblast_Read(afp, &msa2)) != eslOK) esl_fatal("psiblast good file test %d failed: msa read, text", testnumber);
if (msa2->nseq != expected_nseq || msa2->alen != expected_alen) esl_fatal("psiblast good file test %d failed: nseq/alen", testnumber);
if (esl_msa_Validate(msa2, NULL) != eslOK) esl_fatal("psiblast good file test %d failed: msa2 invalid", testnumber);
eslx_msafile_Close(afp);
/* write it back out to a new tmpfile (text write) */
if ( (status = esl_tmpfile_named(tmpfile2, &ofp)) != eslOK) esl_fatal("psiblast good file test %d failed: tmpfile creation", testnumber);
if ( (status = esl_msafile_psiblast_Write(ofp, msa2)) != eslOK) esl_fatal("psiblast good file test %d failed: msa write, text", testnumber);
fclose(ofp);
esl_msa_Destroy(msa2);
/* open and read it in digital mode */
if ( (status = eslx_msafile_Open(&abc, tmpfile1, NULL, eslMSAFILE_PSIBLAST, NULL, &afp)) != eslOK) esl_fatal("psiblast good file test %d failed: 2nd digital mode open", testnumber);
if ( (status = esl_msafile_psiblast_Read(afp, &msa2)) != eslOK) esl_fatal("psiblast good file test %d failed: 2nd digital msa read", testnumber);
if (esl_msa_Validate(msa2, NULL) != eslOK) esl_fatal("psiblast good file test %d failed: msa2 invalid", testnumber);
eslx_msafile_Close(afp);
/* this msa <msa2> should be identical to <msa1> */
if (esl_msa_Compare(msa1, msa2) != eslOK) esl_fatal("psiblast good file test %d failed: msa compare", testnumber);
remove(tmpfile1);
remove(tmpfile2);
esl_msa_Destroy(msa1);
esl_msa_Destroy(msa2);
esl_alphabet_Destroy(abc);
}
static void
read_test_msas_digital(char *pbfile, char *stkfile)
{
char msg[] = "PSIBLAST msa digital read unit test failed";
ESL_ALPHABET *abc = NULL;
ESLX_MSAFILE *afp1 = NULL;
ESLX_MSAFILE *afp2 = NULL;
ESL_MSA *msa1, *msa2, *msa3, *msa4;
FILE *pbfp, *stkfp;
char pbfile2[32] = "esltmppb2XXXXXX";
char stkfile2[32] = "esltmpstk2XXXXXX";
if ( eslx_msafile_Open(&abc, pbfile, NULL, eslMSAFILE_PSIBLAST, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( !abc || abc->type != eslAMINO) esl_fatal(msg);
if ( eslx_msafile_Open(&abc, stkfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Read (afp1, &msa1) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa2) != eslOK) esl_fatal(msg);
if ( esl_msa_Compare(msa1, msa2) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Read (afp1, &msa3) != eslEOF) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa3) != eslEOF) esl_fatal(msg);
eslx_msafile_Close(afp2);
eslx_msafile_Close(afp1);
/* Now write stk to psiblast file, and vice versa; then retest */
if ( esl_tmpfile_named(pbfile2, &pbfp) != eslOK) esl_fatal(msg);
if ( esl_tmpfile_named(stkfile2, &stkfp) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Write (pbfp, msa2) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Write(stkfp, msa1, eslMSAFILE_STOCKHOLM) != eslOK) esl_fatal(msg);
fclose(pbfp);
fclose(stkfp);
if ( eslx_msafile_Open(&abc, pbfile2, NULL, eslMSAFILE_PSIBLAST, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( eslx_msafile_Open(&abc, stkfile2, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Read (afp1, &msa3) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa4) != eslOK) esl_fatal(msg);
if ( esl_msa_Compare(msa3, msa4) != eslOK) esl_fatal(msg);
remove(pbfile2);
remove(stkfile2);
eslx_msafile_Close(afp2);
eslx_msafile_Close(afp1);
esl_msa_Destroy(msa1);
esl_msa_Destroy(msa2);
esl_msa_Destroy(msa3);
esl_msa_Destroy(msa4);
esl_alphabet_Destroy(abc);
}
int
profillic_eslx_msafile_Read(ESLX_MSAFILE *afp, ESL_MSA **ret_msa, ProfileType * profile_ptr)
{
ESL_MSA *msa = NULL;
int status = eslOK;
#ifdef eslAUGMENT_SSI
esl_pos_t offset = esl_buffer_GetOffset(afp->bf);
#endif
switch (afp->format) {
case eslMSAFILE_A2M: if ((status = esl_msafile_a2m_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_AFA: if ((status = esl_msafile_afa_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_CLUSTAL: if ((status = esl_msafile_clustal_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_CLUSTALLIKE: if ((status = esl_msafile_clustal_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_PFAM: if ((status = esl_msafile_stockholm_Read(afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_PHYLIP: if ((status = esl_msafile_phylip_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_PHYLIPS: if ((status = esl_msafile_phylip_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_PSIBLAST: if ((status = esl_msafile_psiblast_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_SELEX: if ((status = esl_msafile_selex_Read (afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_STOCKHOLM: if ((status = esl_msafile_stockholm_Read(afp, &msa)) != eslOK) goto ERROR; break;
case eslMSAFILE_PROFILLIC: if ((status = profillic_esl_msafile_profile_Read(afp, &msa, profile_ptr)) != eslOK) goto ERROR; break;
default: ESL_EXCEPTION(eslEINCONCEIVABLE, "no such msa file format"); break;
}
#ifdef eslAUGMENT_SSI
msa->offset = offset;
#endif
*ret_msa = msa;
return eslOK;
ERROR:
if (msa) esl_msa_Destroy(msa);
*ret_msa = NULL;
return status;
}
static void
read_test_msas_text(char *pbfile, char *stkfile)
{
char msg[] = "PSIBLAST msa text-mode read unit test failed";
ESLX_MSAFILE *afp1 = NULL;
ESLX_MSAFILE *afp2 = NULL;
ESL_MSA *msa1, *msa2, *msa3, *msa4;
FILE *pbfp, *stkfp;
char pbfile2[32] = "esltmppb2XXXXXX";
char stkfile2[32] = "esltmpstk2XXXXXX";
/* vvvv-- everything's the same as the digital utest except these NULLs */
if ( eslx_msafile_Open(NULL, pbfile, NULL, eslMSAFILE_PSIBLAST, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( eslx_msafile_Open(NULL, stkfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Read (afp1, &msa1) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa2) != eslOK) esl_fatal(msg);
if ( esl_msa_Compare(msa1, msa2) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Read (afp1, &msa3) != eslEOF) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa3) != eslEOF) esl_fatal(msg);
eslx_msafile_Close(afp2);
eslx_msafile_Close(afp1);
if ( esl_tmpfile_named(pbfile2, &pbfp) != eslOK) esl_fatal(msg);
if ( esl_tmpfile_named(stkfile2, &stkfp) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Write (pbfp, msa2) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Write(stkfp, msa1, eslMSAFILE_STOCKHOLM) != eslOK) esl_fatal(msg);
fclose(pbfp);
fclose(stkfp);
if ( eslx_msafile_Open(NULL, pbfile2, NULL, eslMSAFILE_PSIBLAST, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( eslx_msafile_Open(NULL, stkfile2, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_psiblast_Read (afp1, &msa3) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa4) != eslOK) esl_fatal(msg);
if ( esl_msa_Compare(msa3, msa4) != eslOK) esl_fatal(msg);
remove(pbfile2);
remove(stkfile2);
eslx_msafile_Close(afp2);
eslx_msafile_Close(afp1);
esl_msa_Destroy(msa1);
esl_msa_Destroy(msa2);
esl_msa_Destroy(msa3);
esl_msa_Destroy(msa4);
}
int
main(int argc, char **argv)
{
char *filename = argv[1];
int fmt = eslMSAFILE_PSIBLAST;
ESLX_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
int status;
if ( (status = eslx_msafile_Open(NULL, filename, NULL, fmt, NULL, &afp)) != eslOK) eslx_msafile_OpenFailure(afp, status);
if ( (status = esl_msafile_psiblast_Read(afp, &msa)) != eslOK) eslx_msafile_ReadFailure(afp, status);
printf("%6d seqs, %5d columns\n", msa->nseq, (int) msa->alen);
esl_msafile_psiblast_Write(stdout, msa);
esl_msa_Destroy(msa);
eslx_msafile_Close(afp);
exit(0);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *filename = esl_opt_GetArg(go, 1);
int infmt = eslMSAFILE_UNKNOWN;
ESL_ALPHABET *abc = NULL;
ESLX_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
int status;
if (esl_opt_GetBoolean(go, "-1")) infmt = eslMSAFILE_PSIBLAST; /* override format autodetection */
if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA);
else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO);
/* Text mode: pass NULL for alphabet.
* Digital mode: pass ptr to expected ESL_ALPHABET; and if abc=NULL, alphabet is guessed
*/
if (esl_opt_GetBoolean(go, "-t")) status = eslx_msafile_Open(NULL, filename, NULL, infmt, NULL, &afp);
else status = eslx_msafile_Open(&abc, filename, NULL, infmt, NULL, &afp);
if (status != eslOK) eslx_msafile_OpenFailure(afp, status);
if ((status = esl_msafile_psiblast_Read(afp, &msa)) != eslOK)
eslx_msafile_ReadFailure(afp, status);
printf("alphabet: %s\n", (abc ? esl_abc_DecodeType(abc->type) : "none (text mode)"));
printf("# of seqs: %d\n", msa->nseq);
printf("# of cols: %d\n", (int) msa->alen);
printf("\n");
if (! esl_opt_GetBoolean(go, "-q"))
esl_msafile_psiblast_Write(stdout, msa);
esl_msa_Destroy(msa);
eslx_msafile_Close(afp);
if (abc) esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
exit(0);
}
