/* Mask sequences in a sequence flatfile. * * SRE, Sat Oct 31 09:58:56 2009 [Janelia] * SVN $Id: esl-mask.c 509 2010-02-07 22:56:55Z eddys $ */ #include "esl_config.h" #include #include #include #include #include "easel.h" #include "esl_fileparser.h" #include "esl_getopts.h" #include "esl_sq.h" #include "esl_sqio.h" static char banner[] = "mask sequences in a sequence file"; static char usage[] = "[options] "; static void cmdline_failure(char *argv0, char *format, ...) { va_list argp; va_start(argp, format); vfprintf(stderr, format, argp); va_end(argp); esl_usage(stdout, argv0, usage); printf("\nTo see more help on available options, do %s -h\n\n", argv0); exit(1); } static void cmdline_help(char *argv0, ESL_GETOPTS *go) { esl_banner(stdout, argv0, banner); esl_usage (stdout, argv0, usage); puts("\n where general options are:"); esl_opt_DisplayHelp(stdout, go, 1, 2, 80); puts(""); puts("The is a sequence file in any accepted format, such as FASTA."); puts("It may be indexed (see esl-sfetch --index) for faster performance."); puts(""); puts("The is a space-delimited file; each data line with 3 columns:"); puts(" field 1: to fetch from "); puts(" field 2: coordinate for mask operation, 1..n"); puts(" field 3: coordinate for mask operation, 1..n"); puts("Lines starting with # are comments, and ignored.)"); puts(""); exit(0); } static ESL_OPTIONS options[] = { /* name type default env range togs reqs incomp help docgroup */ { "-h", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "help; show brief info on version and usage", 1 }, { "-o", eslARG_OUTFILE,FALSE, NULL, NULL, NULL, NULL, NULL, "output masked sequences to file instead of stdout", 1 }, { "-r", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "reverse: mask exclusive of .., not inclusive", 1 }, { "-R", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "random access: fetch seqs from ssi-indexed ", 1 }, { "-l", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, "-m", "convert masked residues to lower case", 1 }, { "-m", eslARG_CHAR, NULL, NULL, NULL, NULL, NULL, "-l", "convert masked residues to character ", 1 }, { "-x", eslARG_INT, NULL, NULL, NULL, NULL, NULL, NULL, "mask additional residues beyond ,", 1 }, { "--informat", eslARG_STRING, FALSE, NULL, NULL, NULL, NULL, NULL, "specify that input file is in format ", 1 }, { 0,0,0,0,0,0,0,0,0,0 }, }; 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 : 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 && sqfp->data.ascii.ssi == NULL) cmdline_failure(argv[0], "-R option (random access/fetching) requires %s to be SSI indexed\n", seqfile); /* Open the */ 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 ****************************************************************************/ /* Read one data line at a time from the ; * parse into data fields */ 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 is SSI indexed, try to reposition it and read 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; and 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 and 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 , 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; }