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/* i/o of multiple sequence alignment files in "aligned FASTA" format
*
* Contents:
* 1. API for reading/writing AFA format
* 2. Unit tests.
* 3. Test driver.
* 4. Examples.
*/
#include "esl_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_mem.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msafile_afa.h"
/*****************************************************************
*# 1. API for reading/writing AFA format
*****************************************************************/
/* Function: esl_msafile_afa_SetInmap()
* Synopsis: Set input map for aligned FASTA format.
*
* Purpose: Set the <afp->inmap> for aligned FASTA format.
*
* Text mode accepts any <isgraph()> character.
* Digital mode enforces the usual Easel alphabets.
*
* We skip spaces in input lines of aligned FASTA format;
* map ' ' to <eslDSQ_IGNORED>.
*/
int
esl_msafile_afa_SetInmap(ESL_MSAFILE *afp)
{
int sym;
if (afp->abc)
{
for (sym = 0; sym < 128; sym++)
afp->inmap[sym] = afp->abc->inmap[sym];
afp->inmap[0] = esl_abc_XGetUnknown(afp->abc);
}
if (! afp->abc)
{
for (sym = 1; sym < 128; sym++)
afp->inmap[sym] = (isgraph(sym) ? sym : eslDSQ_ILLEGAL);
afp->inmap[0] = '?';
}
afp->inmap[' '] = eslDSQ_IGNORED;
return eslOK;
}
/* Function: esl_msafile_afa_GuessAlphabet()
* Synopsis: Guess the alphabet of an open AFA MSA file.
*
* Purpose: Guess the alpbabet of the sequences in open
* AFA format MSA file <afp>.
*
* On a normal return, <*ret_type> is set to <eslDNA>,
* <eslRNA>, or <eslAMINO>, and <afp> is reset to its
* original position.
*
* Args: afp - open AFA format MSA file
* ret_type - RETURN: <eslDNA>, <eslRNA>, or <eslAMINO>
*
* Returns: <eslOK> on success.
* <eslENOALPHABET> if alphabet type can't be determined.
* In either case, <afp> is rewound to the position it
* started at.
*
* Throws: <eslEMEM> on allocation error.
* <eslESYS> on failures of fread() or other system calls
*
* Note: Essentially identical to <esl_msafile_a2m_GuessAlphabet()>,
* but we provide both versions because design calls for
* modularity/separability of parsers.
*/
int
esl_msafile_afa_GuessAlphabet(ESL_MSAFILE *afp, int *ret_type)
{
int alphatype = eslUNKNOWN;
esl_pos_t anchor = -1;
int threshold[3] = { 500, 5000, 50000 }; /* we check after 500, 5000, 50000 residues; else we go to EOF */
int nsteps = 3;
int step = 0;
int nres = 0;
int x;
int64_t ct[26];
char *p;
esl_pos_t n, pos;
int status;
for (x = 0; x < 26; x++) ct[x] = 0;
anchor = esl_buffer_GetOffset(afp->bf);
if ((status = esl_buffer_SetAnchor(afp->bf, anchor)) != eslOK) { status = eslEINCONCEIVABLE; goto ERROR; } /* [eslINVAL] can't happen here */
while ( (status = esl_buffer_GetLine(afp->bf, &p, &n)) == eslOK)
{
while (n && isspace(*p)) { p++; n--; }
if (!n || *p == '>') continue;
for (pos = 0; pos < n; pos++)
if (isalpha(p[pos])) {
x = toupper(p[pos]) - 'A';
ct[x]++;
nres++;
}
/* try to stop early, checking after 500, 5000, and 50000 residues: */
if (step < nsteps && nres > threshold[step]) {
if ((status = esl_abc_GuessAlphabet(ct, &alphatype)) == eslOK) goto DONE; /* (eslENOALPHABET) */
step++;
}
}
if (status != eslEOF) goto ERROR; /* [eslEMEM,eslESYS,eslEINCONCEIVABLE] */
status = esl_abc_GuessAlphabet(ct, &alphatype); /* (eslENOALPHABET) */
/* deliberate flowthrough...*/
DONE:
esl_buffer_SetOffset(afp->bf, anchor); /* Rewind to where we were. */
esl_buffer_RaiseAnchor(afp->bf, anchor);
*ret_type = alphatype;
return status;
ERROR:
if (anchor != -1) {
esl_buffer_SetOffset(afp->bf, anchor);
esl_buffer_RaiseAnchor(afp->bf, anchor);
}
*ret_type = eslUNKNOWN;
return status;
}
/* Function: esl_msafile_afa_Read()
* Synopsis: Read in an aligned FASTA format alignment.
*
* Purpose: Read an MSA from an open <ESL_MSAFILE> <afp>,
* parsing for aligned FASTA format. Create
* a new MSA, and return a ptr to that alignment
* in <*ret_msa>. Caller is responsible for free'ing
* this <ESL_MSA>.
*
* Args: afp - open <ESL_MSAFILE>
* ret_msa - RETURN: newly parsed <ESL_MSA>
*
* Returns: <eslOK> on success. <*ret_msa> is set to the newly
* allocated MSA, and <afp> is at EOF.
*
* <eslEOF> if no (more) alignment data are found in
* <afp>;, and <afp> is returned at EOF.
*
* <eslEFORMAT> on a parse error. <*ret_msa> is set to
* <NULL>. <afp> contains information sufficient for
* constructing useful diagnostic output:
* | <afp->errmsg> | user-directed error message |
* | <afp->linenumber> | line # where error was detected |
* | <afp->line> | offending line (not NUL-term) |
* | <afp->n> | length of offending line |
* | <afp->bf->filename> | name of the file |
* and <afp> is poised at the start of the following line,
* so (in principle) the caller could try to resume
* parsing.
*
* Throws: <eslEMEM> - an allocation failed.
* <eslESYS> - a system call such as fread() failed
* <eslEINCONCEIVABLE> - "impossible" corruption
* On these, <*ret_msa> is returned <NULL>, and the state of
* <afp> is undefined.
*/
int
esl_msafile_afa_Read(ESL_MSAFILE *afp, ESL_MSA **ret_msa)
{
ESL_MSA *msa = NULL;
int idx = 0;
int64_t alen = 0;
int64_t this_alen = 0;
char *p, *tok;
esl_pos_t n, ntok;
int status;
ESL_DASSERT1( (afp->format == eslMSAFILE_AFA) );
afp->errmsg[0] = '\0'; /* Blank the error message. */
if (afp->abc && (msa = esl_msa_CreateDigital(afp->abc, 16, -1)) == NULL) { status = eslEMEM; goto ERROR; }
if (! afp->abc && (msa = esl_msa_Create( 16, -1)) == NULL) { status = eslEMEM; goto ERROR; }
/* skip leading blank lines in file */
while ( (status = esl_msafile_GetLine(afp, &p, &n)) == eslOK && esl_memspn(afp->line, afp->n, " \t") == afp->n) ;
if (status != eslOK) goto ERROR; /* includes normal EOF */
/* tolerate sloppy space at start of line */
while (n && isspace(*p)) { p++; n--; }
if (*p != '>') ESL_XFAIL(eslEFORMAT, afp->errmsg, "expected aligned FASTA name/desc line starting with >");
do {
if (n <= 1 || *p != '>' ) ESL_XFAIL(eslEFORMAT, afp->errmsg, "expected aligned FASTA name/desc line starting with >");
p++; n--; /* advance past > */
if ( (status = esl_memtok(&p, &n, " \t", &tok, &ntok)) != eslOK) ESL_XFAIL(eslEFORMAT, afp->errmsg, "no name found for aligned FASTA record");
if (idx >= msa->sqalloc && (status = esl_msa_Expand(msa)) != eslOK) goto ERROR;
if ( (status = esl_msa_SetSeqName (msa, idx, tok, ntok)) != eslOK) goto ERROR;
if (n && (status = esl_msa_SetSeqDescription(msa, idx, p, n)) != eslOK) goto ERROR;
/* The code below will do a realloc on every line. Possible optimization: once you know
* alen (from first sequence), allocate subsequent seqs once, use noalloc versions of
* esl_strmapcat/esl_abc_dsqcat(). Requires implementing protection against overrun, if
* input is bad and a sequence is too long. Could gain ~25% or so that way (quickie
* test on PF00005 Full)
*/
this_alen = 0;
while ((status = esl_msafile_GetLine(afp, &p, &n)) == eslOK)
{
while (n && isspace(*p)) { p++; n--; } /* tolerate and skip leading whitespace on line */
if (n == 0) continue; /* tolerate and skip blank lines */
if (*p == '>') break;
if (msa->abc) { status = esl_abc_dsqcat(afp->inmap, &(msa->ax[idx]), &this_alen, p, n); }
if (! msa->abc) { status = esl_strmapcat (afp->inmap, &(msa->aseq[idx]), &this_alen, p, n); }
if (status == eslEINVAL) ESL_XFAIL(eslEFORMAT, afp->errmsg, "one or more invalid sequence characters");
else if (status != eslOK) goto ERROR;
}
if (this_alen == 0) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence %s has alen %" PRId64 , msa->sqname[idx], this_alen);
if (alen && alen != this_alen) ESL_XFAIL(eslEFORMAT, afp->errmsg, "sequence %s has alen %" PRId64 "; expected %" PRId64, msa->sqname[idx], this_alen, alen);
alen = this_alen;
idx++;
} while (status == eslOK); /* normally ends on eslEOF. */
msa->nseq = idx;
msa->alen = alen;
if (( status = esl_msa_SetDefaultWeights(msa)) != eslOK) goto ERROR;
*ret_msa = msa;
return eslOK;
ERROR:
if (msa) esl_msa_Destroy(msa);
*ret_msa = NULL;
return status;
}
/* Function: esl_msafile_afa_Write()
* Synopsis: Write an aligned FASTA format alignment file to a stream.
*
* Purpose: Write alignment <msa> in aligned FASTA format to a stream
* <fp>.
*
* If <msa> is in text mode, residues and gaps are written
* exactly as they appear in the data structure. If <msa>
* is digital, residues are in uppercase and all gaps are
* dots (.). Dots are preferred to dashes because it
* minimizes confusion with A2M format.
*
* Args: fp - open stream to write to
* msa - MSA to write
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any system write failure, such as filled disk.
*/
int
esl_msafile_afa_Write(FILE *fp, const ESL_MSA *msa)
{
int i;
int64_t pos;
char buf[61];
int acpl; /* actual number of characters per line */
for (i = 0; i < msa->nseq; i++)
{
if (fprintf(fp, ">%s", msa->sqname[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
if (msa->sqacc != NULL && msa->sqacc[i] != NULL) { if (fprintf(fp, " %s", msa->sqacc[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed"); }
if (msa->sqdesc != NULL && msa->sqdesc[i] != NULL) { if (fprintf(fp, " %s", msa->sqdesc[i]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed"); }
if (fputc('\n', fp) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
pos = 0;
while (pos < msa->alen)
{
acpl = (msa->alen - pos > 60)? 60 : msa->alen - pos;
if (msa->abc) esl_abc_TextizeN(msa->abc, msa->ax[i] + pos + 1, acpl, buf);
if (! msa->abc) strncpy(buf, msa->aseq[i] + pos, acpl);
buf[acpl] = '\0';
if (fprintf(fp, "%s\n", buf) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "afa msa file write failed");
pos += 60;
}
}
return eslOK;
}
/*****************************************************************
* 2. Unit tests.
*****************************************************************/
#ifdef eslMSAFILE_AFA_TESTDRIVE
/* a standard globin example, dusted with evil:
* 1. \r\n DOS line terminators;
* 2. extra blank lines and whitespace
* 3. unusual but legal residues
*/
static void
utest_write_good1(FILE *ofp, int *ret_alphatype, int *ret_nseq, int *ret_alen)
{
fputs(" \r\n", ofp);
fputs("> MYG_PHYCA description \r\n", ofp);
fputs("--------V-LSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT\r\n", ofp);
fputs("EAEMKASEDLKKHGVTVLTALGAILKKKGH---HEABJZOUX*SHATKHKIPIKYLEFIS \r\n", ofp);
fputs("EAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG\r\n", ofp);
fputs(" \r\n", ofp);
fputs(">GLB5_PETMA\r\n", ofp);
fputs("PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT\r\n", ofp);
fputs("ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA\r\n", ofp);
fputs("AVI---------ADTVAAGDAGFEKLMSMICILLRSAY-------\r\n", ofp);
fputs(">HBB_HUMAN\r\n", ofp);
fputs("--------VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST\r\n", ofp);
fputs("PDAVMGNPKVKAHGKKVLGAFSDGLAHLDN---LKGTFATLSELHCDKLHVDPENFRLLG\r\n", ofp);
fputs("NVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------\r\n", ofp);
fputs(">HBA_HUMAN\r\n", ofp);
fputs("--------V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-----\r\n", ofp);
fputs("-DLSHGSAQVKGHGKKVADALTNAVAHVDD---MPNALSALSDLHAHKLRVDPVNFKLLS\r\n", ofp);
fputs("HCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------\r\n", ofp);
fputs(" \r\n", ofp);
*ret_alphatype = eslAMINO;
*ret_nseq = 4;
*ret_alen = 165;
}
static void
utest_goodfile(char *filename, int testnumber, int expected_alphatype, int expected_nseq, int expected_alen)
{
ESL_ALPHABET *abc = NULL;
ESL_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 */
if ( (status = esl_msafile_Open(&abc, filename, NULL, eslMSAFILE_UNKNOWN, NULL, &afp)) != eslOK) esl_fatal("afa good file test %d failed: digital open", testnumber);
if (afp->format != eslMSAFILE_AFA) esl_fatal("afa good file test %d failed: format autodetection", testnumber);
if (abc->type != expected_alphatype) esl_fatal("afa good file test %d failed: alphabet autodetection", testnumber);
/* This is a digital read, using <abc>. */
if ( (status = esl_msafile_afa_Read(afp, &msa1)) != eslOK) esl_fatal("afa good file test %d failed: msa read, digital", testnumber);
if (msa1->nseq != expected_nseq || msa1->alen != expected_alen) esl_fatal("afa good file test %d failed: nseq/alen", testnumber);
if (esl_msa_Validate(msa1, NULL) != eslOK) esl_fatal("afa good file test %d failed: msa invalid", testnumber);
esl_msafile_Close(afp);
/* write it back out to a new tmpfile (digital write) */
if ( (status = esl_tmpfile_named(tmpfile1, &ofp)) != eslOK) esl_fatal("afa good file test %d failed: tmpfile creation", testnumber);
if ( (status = esl_msafile_afa_Write(ofp, msa1)) != eslOK) esl_fatal("afa 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 = esl_msafile_Open(NULL, tmpfile1, NULL, eslMSAFILE_AFA, NULL, &afp)) != eslOK) esl_fatal("afa good file test %d failed: text mode open", testnumber);
if ( (status = esl_msafile_afa_Read(afp, &msa2)) != eslOK) esl_fatal("afa good file test %d failed: msa read, text", testnumber);
if (msa2->nseq != expected_nseq || msa2->alen != expected_alen) esl_fatal("afa good file test %d failed: nseq/alen", testnumber);
if (esl_msa_Validate(msa2, NULL) != eslOK) esl_fatal("afa good file test %d failed: msa invalid", testnumber);
esl_msafile_Close(afp);
/* write it back out to a new tmpfile (text write) */
if ( (status = esl_tmpfile_named(tmpfile2, &ofp)) != eslOK) esl_fatal("afa good file test %d failed: tmpfile creation", testnumber);
if ( (status = esl_msafile_afa_Write(ofp, msa2)) != eslOK) esl_fatal("afa good file test %d failed: msa write, text", testnumber);
fclose(ofp);
esl_msa_Destroy(msa2);
/* open and read it in digital mode */
if ( (status = esl_msafile_Open(&abc, tmpfile1, NULL, eslMSAFILE_AFA, NULL, &afp)) != eslOK) esl_fatal("afa good file test %d failed: 2nd digital mode open", testnumber);
if ( (status = esl_msafile_afa_Read(afp, &msa2)) != eslOK) esl_fatal("afa good file test %d failed: 2nd digital msa read", testnumber);
if (esl_msa_Validate(msa2, NULL) != eslOK) esl_fatal("afa good file test %d failed: msa invalid", testnumber);
esl_msafile_Close(afp);
/* this msa <msa2> should be identical to <msa1> */
if (esl_msa_Compare(msa1, msa2) != eslOK) esl_fatal("afa 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
write_test_msas(FILE *ofp1, FILE *ofp2)
{
fprintf(ofp1, "\n");
fprintf(ofp1, ">seq1 description line for seq1\n");
fprintf(ofp1, "..acdefghiklmnpqrstvwy\n");
fprintf(ofp1, "ACDEFGHIKLMNPQRSTVWY..\n");
fprintf(ofp1, "\n");
fprintf(ofp1, ">seq2 description line for seq2\n");
fprintf(ofp1, "..acdefghiklmnpqrstv--\n");
fprintf(ofp1, "ACDEFGHIKLMNPQRSTVWYyy\n");
fprintf(ofp1, " >seq3\n");
fprintf(ofp1, "aaacdefghiklmnpqrstv--ACDEFGHIKLMNPQRSTVWY..\n");
fprintf(ofp1, ">seq4\n");
fprintf(ofp1, "..acdefghiklm\n");
fprintf(ofp1, "npqrstvwyACDE\n");
fprintf(ofp1, "FGHIKLMNPQRSTVWY..\n");
fprintf(ofp2, "# STOCKHOLM 1.0\n");
fprintf(ofp2, "\n");
fprintf(ofp2, "#=GS seq1 DE description line for seq1\n");
fprintf(ofp2, "#=GS seq2 DE description line for seq2\n");
fprintf(ofp2, "\n");
fprintf(ofp2, "seq1 ..acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY..\n");
fprintf(ofp2, "seq2 ..acdefghiklmnpqrstv--ACDEFGHIKLMNPQRSTVWYyy\n");
fprintf(ofp2, "seq3 aaacdefghiklmnpqrstv--ACDEFGHIKLMNPQRSTVWY..\n");
fprintf(ofp2, "seq4 ..acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY..\n");
fprintf(ofp2, "//\n");
}
static void
read_test_msas_digital(char *afafile, char *stkfile)
{
char msg[] = "aligned FASTA msa digital read unit test failed";
ESL_ALPHABET *abc = NULL;
ESL_MSAFILE *afp1 = NULL;
ESL_MSAFILE *afp2 = NULL;
ESL_MSA *msa1, *msa2, *msa3, *msa4;
FILE *afafp, *stkfp;
char afafile2[32] = "esltmpafa2XXXXXX";
char stkfile2[32] = "esltmpstk2XXXXXX";
if ( esl_msafile_Open(&abc, afafile, NULL, eslMSAFILE_AFA, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( !abc || abc->type != eslAMINO) esl_fatal(msg);
if ( esl_msafile_Open(&abc, stkfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_afa_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_afa_Read (afp1, &msa3) != eslEOF) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa3) != eslEOF) esl_fatal(msg);
esl_msafile_Close(afp2);
esl_msafile_Close(afp1);
/* Now write stk to afa file, and vice versa; then retest */
if ( esl_tmpfile_named(afafile2, &afafp) != eslOK) esl_fatal(msg);
if ( esl_tmpfile_named(stkfile2, &stkfp) != eslOK) esl_fatal(msg);
if ( esl_msafile_afa_Write (afafp, msa2) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Write(stkfp, msa1, eslMSAFILE_STOCKHOLM) != eslOK) esl_fatal(msg);
fclose(afafp);
fclose(stkfp);
if ( esl_msafile_Open(&abc, afafile2, NULL, eslMSAFILE_AFA, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( esl_msafile_Open(&abc, stkfile2, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_afa_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(afafile2);
remove(stkfile2);
esl_msafile_Close(afp2);
esl_msafile_Close(afp1);
esl_msa_Destroy(msa1);
esl_msa_Destroy(msa2);
esl_msa_Destroy(msa3);
esl_msa_Destroy(msa4);
esl_alphabet_Destroy(abc);
}
static void
read_test_msas_text(char *afafile, char *stkfile)
{
char msg[] = "aligned FASTA msa text-mode read unit test failed";
ESL_MSAFILE *afp1 = NULL;
ESL_MSAFILE *afp2 = NULL;
ESL_MSA *msa1, *msa2, *msa3, *msa4;
FILE *afafp, *stkfp;
char afafile2[32] = "esltmpafa2XXXXXX";
char stkfile2[32] = "esltmpstk2XXXXXX";
/* vvvv-- everything's the same as the digital utest except these NULLs */
if ( esl_msafile_Open(NULL, afafile, NULL, eslMSAFILE_AFA, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( esl_msafile_Open(NULL, stkfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_afa_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_afa_Read (afp1, &msa3) != eslEOF) esl_fatal(msg);
if ( esl_msafile_stockholm_Read(afp2, &msa3) != eslEOF) esl_fatal(msg);
esl_msafile_Close(afp2);
esl_msafile_Close(afp1);
if ( esl_tmpfile_named(afafile2, &afafp) != eslOK) esl_fatal(msg);
if ( esl_tmpfile_named(stkfile2, &stkfp) != eslOK) esl_fatal(msg);
if ( esl_msafile_afa_Write (afafp, msa2) != eslOK) esl_fatal(msg);
if ( esl_msafile_stockholm_Write(stkfp, msa1, eslMSAFILE_STOCKHOLM) != eslOK) esl_fatal(msg);
fclose(afafp);
fclose(stkfp);
if ( esl_msafile_Open(NULL, afafile2, NULL, eslMSAFILE_AFA, NULL, &afp1) != eslOK) esl_fatal(msg);
if ( esl_msafile_Open(NULL, stkfile2, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2) != eslOK) esl_fatal(msg);
if ( esl_msafile_afa_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(afafile2);
remove(stkfile2);
esl_msafile_Close(afp2);
esl_msafile_Close(afp1);
esl_msa_Destroy(msa1);
esl_msa_Destroy(msa2);
esl_msa_Destroy(msa3);
esl_msa_Destroy(msa4);
}
#endif /*eslMSAFILE_AFA_TESTDRIVE*/
/*---------------------- end, unit tests ------------------------*/
/*****************************************************************
* 3. Test driver.
*****************************************************************/
#ifdef eslMSAFILE_AFA_TESTDRIVE
/* compile: gcc -g -Wall -I. -L. -o esl_msafile_afa_utest -DeslMSAFILE_AFA_TESTDRIVE esl_msafile_afa.c -leasel -lm
* (gcov): gcc -g -Wall -fprofile-arcs -ftest-coverage -I. -L. -o esl_msafile_afa_utest -DeslMSAFILE_AFA_TESTDRIVE esl_msafile_afa.c -leasel -lm
* run: ./esl_msafile_afa_utest
*/
#include "esl_config.h"
#include <stdio.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_random.h"
#include "esl_msafile.h"
#include "esl_msafile_afa.h"
static ESL_OPTIONS options[] = {
/* name type default env range togs reqs incomp help docgrp */
{"-h", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "show help and usage", 0},
{ 0,0,0,0,0,0,0,0,0,0},
};
static char usage[] = "[-options]";
static char banner[] = "test driver for AFA MSA format module";
int
main(int argc, char **argv)
{
char msg[] = "aligned FASTA MSA i/o module test driver failed";
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage);
char afafile[32] = "esltmpafaXXXXXX";
char stkfile[32] = "esltmpstkXXXXXX";
FILE *afafp, *stkfp;
int testnumber;
int ngoodtests = 1;
char tmpfile[32];
FILE *ofp;
int expected_alphatype;
int expected_nseq;
int expected_alen;
if ( esl_tmpfile_named(afafile, &afafp) != eslOK) esl_fatal(msg);
if ( esl_tmpfile_named(stkfile, &stkfp) != eslOK) esl_fatal(msg);
write_test_msas(afafp, stkfp);
fclose(afafp);
fclose(stkfp);
read_test_msas_digital(afafile, stkfile);
read_test_msas_text (afafile, stkfile);
/* Various "good" files that should be parsed correctly */
for (testnumber = 1; testnumber <= ngoodtests; testnumber++)
{
strcpy(tmpfile, "esltmpXXXXXX");
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
switch (testnumber) {
case 1: utest_write_good1 (ofp, &expected_alphatype, &expected_nseq, &expected_alen); break;
}
fclose(ofp);
utest_goodfile(tmpfile, testnumber, expected_alphatype, expected_nseq, expected_alen);
remove(tmpfile);
}
remove(afafile);
remove(stkfile);
esl_getopts_Destroy(go);
return 0;
}
#endif /*eslMSAFILE_AFA_TESTDRIVE*/
/*--------------------- end, test driver ------------------------*/
/*****************************************************************
* 4. Examples.
*****************************************************************/
#ifdef eslMSAFILE_AFA_EXAMPLE
/* A full-featured example of reading/writing an MSA in aligned FASTA (AFA) format.
gcc -g -Wall -o esl_msafile_afa_example -I. -L. -DeslMSAFILE_afa_EXAMPLE esl_msafile_afa.c -leasel -lm
./esl_msafile_afa_example <msafile>
*/
/*::cexcerpt::msafile_afa_example::begin::*/
#include <stdio.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msafile_afa.h"
static ESL_OPTIONS options[] = {
/* name type default env range toggles reqs incomp help docgroup*/
{ "-h", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "show brief help on version and usage", 0 },
{ "-1", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "override autodetection; force AFA format", 0 },
{ "-q", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "quieter: don't write msa back, just summary", 0 },
{ "-t", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "use text mode: no digital alphabet", 0 },
{ "--dna", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-t", "specify that alphabet is DNA", 0 },
{ "--rna", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-t", "specify that alphabet is RNA", 0 },
{ "--amino", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-t", "specify that alphabet is protein", 0 },
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
};
static char usage[] = "[-options] <msafile>";
static char banner[] = "example of guessing, reading, writing AFA format";
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;
ESL_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
int status;
if (esl_opt_GetBoolean(go, "-1")) infmt = eslMSAFILE_AFA; /* 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 = esl_msafile_Open(NULL, filename, NULL, infmt, NULL, &afp);
else status = esl_msafile_Open(&abc, filename, NULL, infmt, NULL, &afp);
if (status != eslOK) esl_msafile_OpenFailure(afp, status);
if ((status = esl_msafile_afa_Read(afp, &msa)) != eslOK)
esl_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_afa_Write(stdout, msa);
esl_msa_Destroy(msa);
esl_msafile_Close(afp);
if (abc) esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
exit(0);
}
/*::cexcerpt::msafile_afa_example::end::*/
#endif /*eslMSAFILE_AFA_EXAMPLE*/
#ifdef eslMSAFILE_AFA_EXAMPLE2
/* A minimal example. Read AFA format MSA, in text mode.
gcc -g -Wall -o esl_msafile_afa_example2 -I. -L. -DeslMSAFILE_AFA_EXAMPLE2 esl_msafile_afa.c -leasel -lm
./esl_msafile_afa_example2 <msafile>
*/
/*::cexcerpt::msafile_afa_example2::begin::*/
#include <stdio.h>
#include "easel.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msafile_afa.h"
int
main(int argc, char **argv)
{
char *filename = argv[1];
int fmt = eslMSAFILE_AFA;
ESL_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
int status;
if ( (status = esl_msafile_Open(NULL, filename, NULL, fmt, NULL, &afp)) != eslOK) esl_msafile_OpenFailure(afp, status);
if ( (status = esl_msafile_afa_Read(afp, &msa)) != eslOK) esl_msafile_ReadFailure(afp, status);
printf("%6d seqs, %5d columns\n", msa->nseq, (int) msa->alen);
esl_msafile_afa_Write(stdout, msa);
esl_msa_Destroy(msa);
esl_msafile_Close(afp);
exit(0);
}
/*::cexcerpt::msafile_afa_example2::end::*/
#endif /*eslMSAFILE_AFA_EXAMPLE2*/
/*--------------------- end of examples -------------------------*/
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