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view clustalomega/clustal-omega-1.0.2/src/squid/sqio.c @ 1:bc707542e5de
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| author | clustalomega |
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| date | Thu, 21 Jul 2011 13:35:08 -0400 |
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/***************************************************************** * SQUID - a library of functions for biological sequence analysis * Copyright (C) 1992-2002 Washington University School of Medicine * * This source code is freely distributed under the terms of the * GNU General Public License. See the files COPYRIGHT and LICENSE * for details. *****************************************************************/ /* File: sqio.c * From: ureadseq.c in Don Gilbert's sequence i/o package * * Reads and writes nucleic/protein sequence in various * formats. Data files may have multiple sequences. * * Heavily modified from READSEQ package * Copyright (C) 1990 by D.G. Gilbert * Biology Dept., Indiana University, Bloomington, IN 47405 * email: gilbertd@bio.indiana.edu * Thanks Don! * * SRE: Modifications as noted. Fri Jul 3 09:44:54 1992 * Packaged for squid, Thu Oct 1 10:07:11 1992 * ANSI conversion in full swing, Mon Jul 12 12:22:21 1993 * * CVS $Id: sqio.c,v 1.29 2002/08/26 23:10:52 eddy Exp) * ***************************************************************** * Basic API for single sequence reading: * * SQFILE *sqfp; * char *seqfile; * int format; - see squid.h for formats; example: SQFILE_FASTA * char *seq; * SQINFO sqinfo; * * if ((sqfp = SeqfileOpen(seqfile, format, "BLASTDB")) == NULL) * Die("Failed to open sequence database file %s\n%s\n", seqfile, usage); * while (ReadSeq(sqfp, sqfp->format, &seq, &sqinfo)) { * do_stuff; * FreeSequence(seq, &sqinfo); * } * SeqfileClose(sqfp); * ***************************************************************** */ #include <stdio.h> #include <stdlib.h> #include <string.h> #include <ctype.h> #ifndef SEEK_SET #include <unistd.h> #endif #include "squid.h" #include "msa.h" #include "ssi.h" static void SeqfileGetLine(SQFILE *V); #define kStartLength 500 static char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*"; static char *primenuc = "ACGTUN"; static char *protonly = "EFIPQZ"; static SQFILE *seqfile_open(char *filename, int format, char *env, int ssimode); /* Function: SeqfileOpen() * * Purpose : Open a sequence database file and prepare for reading * sequentially. * * Args: filename - name of file to open * format - format of file * env - environment variable for path (e.g. BLASTDB) * ssimode - -1, SSI_OFFSET_I32, or SSI_OFFSET_I64 * * Returns opened SQFILE ptr, or NULL on failure. */ SQFILE * SeqfileOpen(char *filename, int format, char *env) { return seqfile_open(filename, format, env, -1); } SQFILE * SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode) { return seqfile_open(filename, format, env, ssimode); } static SQFILE * seqfile_open(char *filename, int format, char *env, int ssimode) { SQFILE *dbfp; dbfp = (SQFILE *) MallocOrDie (sizeof(SQFILE)); dbfp->ssimode = ssimode; dbfp->rpl = -1; /* flag meaning "unset" */ dbfp->lastrpl = 0; dbfp->maxrpl = 0; dbfp->bpl = -1; /* flag meaning "unset" */ dbfp->lastbpl = 0; dbfp->maxbpl = 0; /* Open our file handle. * Three possibilities: * 1. normal file open * 2. filename = "-"; read from stdin * 3. filename = "*.gz"; read thru pipe from gzip * If we're reading from stdin or a pipe, we can't reliably * back up, so we can't do two-pass parsers like the interleaved alignment * formats. */ if (strcmp(filename, "-") == 0) { dbfp->f = stdin; dbfp->do_stdin = TRUE; dbfp->do_gzip = FALSE; dbfp->fname = sre_strdup("[STDIN]", -1); } #ifndef SRE_STRICT_ANSI /* popen(), pclose() aren't portable to non-POSIX systems; disable */ else if (Strparse("^.*\\.gz$", filename, 0)) { char cmd[256]; /* Note that popen() will return "successfully" * if file doesn't exist, because gzip works fine * and prints an error! So we have to check for * existence of file ourself. */ if (! FileExists(filename)) Die("%s: file does not exist", filename); if (strlen(filename) + strlen("gzip -dc ") >= 256) Die("filename > 255 char in SeqfileOpen()"); sprintf(cmd, "gzip -dc %s", filename); if ((dbfp->f = popen(cmd, "r")) == NULL) return NULL; dbfp->do_stdin = FALSE; dbfp->do_gzip = TRUE; dbfp->fname = sre_strdup(filename, -1); } #endif /*SRE_STRICT_ANSI*/ else { if ((dbfp->f = fopen(filename, "r")) == NULL && (dbfp->f = EnvFileOpen(filename, env, NULL)) == NULL) return NULL; dbfp->do_stdin = FALSE; dbfp->do_gzip = FALSE; dbfp->fname = sre_strdup(filename, -1); } /* Invoke autodetection if we haven't already been told what * to expect. */ if (format == SQFILE_UNKNOWN) { if (dbfp->do_stdin == TRUE || dbfp->do_gzip) Die("Can't autodetect sequence file format from a stdin or gzip pipe"); format = SeqfileFormat(dbfp->f); if (format == SQFILE_UNKNOWN) Die("Can't determine format of sequence file %s", dbfp->fname); } /* The hack for sequential access of an interleaved alignment file: * read the alignment in, we'll copy sequences out one at a time. */ dbfp->msa = NULL; dbfp->afp = NULL; dbfp->format = format; dbfp->linenumber = 0; dbfp->buf = NULL; dbfp->buflen = 0; if (IsAlignmentFormat(format)) { /* We'll be reading from the MSA interface. Copy our data * to the MSA afp's structure. */ dbfp->afp = MallocOrDie(sizeof(MSAFILE)); dbfp->afp->f = dbfp->f; /* just a ptr, don't close */ dbfp->afp->do_stdin = dbfp->do_stdin; dbfp->afp->do_gzip = dbfp->do_gzip; dbfp->afp->fname = dbfp->fname; /* just a ptr, don't free */ dbfp->afp->format = dbfp->format; /* e.g. format */ dbfp->afp->linenumber = dbfp->linenumber; /* e.g. 0 */ dbfp->afp->buf = NULL; dbfp->afp->buflen = 0; if ((dbfp->msa = MSAFileRead(dbfp->afp)) == NULL) Die("Failed to read any alignment data from file %s", dbfp->fname); /* hack: overload/reuse msa->lastidx; indicates next seq to return upon a ReadSeq() call */ dbfp->msa->lastidx = 0; return dbfp; } /* Load the first line. */ SeqfileGetLine(dbfp); return dbfp; } /* Function: SeqfilePosition() * * Purpose: Move to a particular offset in a seqfile. * Will not work on alignment files. */ void SeqfilePosition(SQFILE *sqfp, SSIOFFSET *offset) { if (sqfp->do_stdin || sqfp->do_gzip || IsAlignmentFormat(sqfp->format)) Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); if (SSISetFilePosition(sqfp->f, offset) != 0) Die("SSISetFilePosition failed, but that shouldn't happen."); SeqfileGetLine(sqfp); } /* Function: SeqfileRewind() * * Purpose: Set a sequence file back to the first sequence. * * Won't work on alignment files. Although it would * seem that it could (just set msa->lastidx back to 0), * that'll fail on "multiple multiple" alignment file formats * (e.g. Stockholm). */ void SeqfileRewind(SQFILE *sqfp) { if (sqfp->do_stdin || sqfp->do_gzip) Die("SeqfileRewind() failed: in a nonrewindable data file or stream"); rewind(sqfp->f); SeqfileGetLine(sqfp); } /* Function: SeqfileLineParameters() * Date: SRE, Thu Feb 15 17:00:41 2001 [St. Louis] * * Purpose: After all the sequences have been read from the file, * but before closing it, retrieve overall bytes-per-line and * residues-per-line info. If non-zero, these mean that * the file contains homogeneous sequence line lengths (except * the last line in each record). * * If either of bpl or rpl is determined to be inhomogeneous, * both are returned as 0. * * Args: *sqfp - an open but fully read sequence file * ret_bpl - RETURN: bytes per line, or 0 if inhomogeneous * ret_rpl - RETURN: residues per line, or 0 if inhomogenous. * * Returns: void */ void SeqfileLineParameters(SQFILE *V, int *ret_bpl, int *ret_rpl) { if (V->rpl > 0 && V->maxrpl == V->rpl && V->bpl > 0 && V->maxbpl == V->bpl) { *ret_bpl = V->bpl; *ret_rpl = V->rpl; } else { *ret_bpl = 0; *ret_rpl = 0; } } void SeqfileClose(SQFILE *sqfp) { /* note: don't test for sqfp->msa being NULL. Now that * we're holding afp open and allowing access to multi-MSA * databases (e.g. Stockholm format, Pfam), msa ends * up being NULL when we run out of alignments. */ if (sqfp->afp != NULL) { if (sqfp->msa != NULL) MSAFree(sqfp->msa); if (sqfp->afp->buf != NULL) free(sqfp->afp->buf); free(sqfp->afp); } #ifndef SRE_STRICT_ANSI /* gunzip functionality only on POSIX systems */ if (sqfp->do_gzip) pclose(sqfp->f); #endif else if (! sqfp->do_stdin) fclose(sqfp->f); if (sqfp->buf != NULL) free(sqfp->buf); if (sqfp->fname != NULL) free(sqfp->fname); free(sqfp); } /* Function: SeqfileGetLine() * Date: SRE, Tue Jun 22 09:15:49 1999 [Sanger Centre] * * Purpose: read a line from a sequence file into V->buf * If the fgets() is NULL, sets V->buf[0] to '\0'. * * Args: V * * Returns: void */ static void SeqfileGetLine(SQFILE *V) { if (V->ssimode >= 0) if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->ssioffset))) Die("SSIGetFilePosition() failed"); if (sre_fgets(&(V->buf), &(V->buflen), V->f) == NULL) *(V->buf) = '\0'; V->linenumber++; } void FreeSequence(char *seq, SQINFO *sqinfo) { if (seq != NULL) free(seq); /* FS, r244, here is potential problem in profile/profile */ if (sqinfo->flags & SQINFO_SS){ if (NULL != sqinfo->ss){ /* FS, r244 -> r245 */ free(sqinfo->ss); } } if (sqinfo->flags & SQINFO_SA){ if (NULL != sqinfo->sa){ /* FS, r244 -> r245 */ free(sqinfo->sa); } } } int SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag) { int len; int pos; /* silently ignore NULL. */ if (sptr == NULL) return 1; while (*sptr == ' ') sptr++; /* ignore leading whitespace */ for (pos = strlen(sptr)-1; pos >= 0; pos--) if (! isspace((int) sptr[pos])) break; sptr[pos+1] = '\0'; /* ignore trailing whitespace */ switch (flag) { case SQINFO_NAME: if (*sptr != '-') { strncpy(sqinfo->name, sptr, SQINFO_NAMELEN-1); sqinfo->name[SQINFO_NAMELEN-1] = '\0'; sqinfo->flags |= SQINFO_NAME; } break; case SQINFO_ID: if (*sptr != '-') { strncpy(sqinfo->id, sptr, SQINFO_NAMELEN-1); sqinfo->id[SQINFO_NAMELEN-1] = '\0'; sqinfo->flags |= SQINFO_ID; } break; case SQINFO_ACC: if (*sptr != '-') { strncpy(sqinfo->acc, sptr, SQINFO_NAMELEN-1); sqinfo->acc[SQINFO_NAMELEN-1] = '\0'; sqinfo->flags |= SQINFO_ACC; } break; case SQINFO_DESC: if (*sptr != '-') { if (sqinfo->flags & SQINFO_DESC) /* append? */ { len = strlen(sqinfo->desc); if (len < SQINFO_DESCLEN-2) /* is there room? */ { strncat(sqinfo->desc, " ", SQINFO_DESCLEN-1-len); len++; strncat(sqinfo->desc, sptr, SQINFO_DESCLEN-1-len); } } else /* else copy */ strncpy(sqinfo->desc, sptr, SQINFO_DESCLEN-1); sqinfo->desc[SQINFO_DESCLEN-1] = '\0'; sqinfo->flags |= SQINFO_DESC; } break; case SQINFO_START: if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; } sqinfo->start = atoi(sptr); if (sqinfo->start != 0) sqinfo->flags |= SQINFO_START; break; case SQINFO_STOP: if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; } sqinfo->stop = atoi(sptr); if (sqinfo->stop != 0) sqinfo->flags |= SQINFO_STOP; break; case SQINFO_OLEN: if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; } sqinfo->olen = atoi(sptr); if (sqinfo->olen != 0) sqinfo->flags |= SQINFO_OLEN; break; default: Die("Invalid flag %d to SetSeqinfoString()", flag); } return 1; } void SeqinfoCopy(SQINFO *sq1, SQINFO *sq2) { sq1->flags = sq2->flags; if (sq2->flags & SQINFO_NAME) strcpy(sq1->name, sq2->name); if (sq2->flags & SQINFO_ID) strcpy(sq1->id, sq2->id); if (sq2->flags & SQINFO_ACC) strcpy(sq1->acc, sq2->acc); if (sq2->flags & SQINFO_DESC) strcpy(sq1->desc, sq2->desc); if (sq2->flags & SQINFO_LEN) sq1->len = sq2->len; if (sq2->flags & SQINFO_START) sq1->start = sq2->start; if (sq2->flags & SQINFO_STOP) sq1->stop = sq2->stop; if (sq2->flags & SQINFO_OLEN) sq1->olen = sq2->olen; if (sq2->flags & SQINFO_TYPE) sq1->type = sq2->type; if (sq2->flags & SQINFO_SS) sq1->ss = Strdup(sq2->ss); if (sq2->flags & SQINFO_SA) sq1->sa = Strdup(sq2->sa); } /* Function: ToDNA() * * Purpose: Convert a sequence to DNA. * U --> T */ void ToDNA(char *seq) { for (; *seq != '\0'; seq++) { if (*seq == 'U') *seq = 'T'; else if (*seq == 'u') *seq = 't'; } } /* Function: ToRNA() * * Purpose: Convert a sequence to RNA. * T --> U */ void ToRNA(char *seq) { for (; *seq != '\0'; seq++) { if (*seq == 'T') *seq = 'U'; else if (*seq == 't') *seq = 'u'; } } /* Function: ToIUPAC() * * Purpose: Convert X's, o's, other junk in a nucleic acid sequence to N's, * to comply with IUPAC code. If is_aseq is TRUE, will allow gap * characters though, so we can call ToIUPAC() on aligned seqs. * * NUCLEOTIDES is defined in squid.h as: * "ACGTUNRYMKSWHBVDacgtunrymkswhbvd" * gap chars allowed by isgap() are defined in squid.h as: * " ._-~" * * WU-BLAST's pressdb will * choke on X's, for instance, necessitating conversion * of certain genome centers' data. */ void ToIUPAC(char *seq, int is_aseq) { if (is_aseq) { for (; *seq != '\0'; seq++) if (strchr(NUCLEOTIDES, *seq) == NULL && ! isgap(*seq)) *seq = 'N'; } else { for (; *seq != '\0'; seq++) if (strchr(NUCLEOTIDES, *seq) == NULL) *seq = 'N'; } } /* Function: addseq() * * Purpose: Add a line of sequence to the growing string in V. * * In the seven supported unaligned formats, all sequence * lines may contain whitespace that must be filtered out; * four formats (PIR, EMBL, Genbank, GCG) include coordinates * that must be filtered out. Thus an (!isdigit && !isspace) * test on each character before we accept it. */ static void addseq(char *s, struct ReadSeqVars *V) { char *s0; char *sq; int rpl; /* valid residues per line */ int bpl; /* characters per line */ if (V->ssimode == -1) { /* Normal mode: keeping the seq */ /* Make sure we have enough room. We know that s is <= buflen, * so just make sure we've got room for a whole new buflen worth * of sequence. */ if (V->seqlen + V->buflen > V->maxseq) { V->maxseq += MAX(V->buflen, kStartLength); V->seq = ReallocOrDie (V->seq, V->maxseq+1); } sq = V->seq + V->seqlen; while (*s != 0) { #ifdef CLUSTALO if (! isdigit((int) *s) && ! isspace((int) *s) && isprint((int) *s)) { #else if (! isdigit((int) *s) && ! isspace((int) *s)) { #endif *sq = *s; sq++; } s++; } V->seqlen = sq - V->seq; } else /* else: indexing mode, discard the seq */ { s0 = s; rpl = 0; while (*s != 0) { if (! isdigit((int) *s) && ! isspace((int) *s)) { rpl++; } s++; } V->seqlen += rpl; bpl = s - s0; /* Keep track of the global rpl, bpl for the file. * This is overly complicated because we have to * allow the last line of each record (e.g. the last addseq() call * on each sequence) to have a different length - and sometimes * we'll have one-line sequence records, too. Thus we only * do something with the global V->rpl when we have *passed over* * a line - we keep the last line's rpl in last_rpl. And because * a file might consist entirely of single-line records, we keep * a third guy, maxrpl, that tells us the maximum rpl of any line * in the file. If we reach the end of file and rpl is still unset, * we'll set it to maxrpl. If we reach eof and rpl is set, but is * less than maxrpl, that's a weird case where a last line in some * record is longer than every other line. */ if (V->rpl != 0) { /* 0 means we already know rpl is invalid */ if (V->lastrpl > 0) { /* we're on something that's not the first line */ if (V->rpl > 0 && V->lastrpl != V->rpl) V->rpl = 0; else if (V->rpl == -1) V->rpl = V->lastrpl; } V->lastrpl = rpl; if (rpl > V->maxrpl) V->maxrpl = rpl; /* make sure we check max length of final lines */ } if (V->bpl != 0) { /* 0 means we already know bpl is invalid */ if (V->lastbpl > 0) { /* we're on something that's not the first line */ if (V->bpl > 0 && V->lastbpl != V->bpl) V->bpl = 0; else if (V->bpl == -1) V->bpl = V->lastbpl; } V->lastbpl = bpl; if (bpl > V->maxbpl) V->maxbpl = bpl; /* make sure we check max length of final lines */ } } /* end of indexing mode of addseq(). */ } static void readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) { int addend = 0; int done = 0; V->seqlen = 0; V->lastrpl = V->lastbpl = 0; if (addfirst) { if (V->ssimode >= 0) V->d_off = V->ssioffset; addseq(V->buf, V); } else if (V->ssimode >= 0) if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->d_off))) Die("SSIGetFilePosition() failed"); do { SeqfileGetLine(V); /* feof() alone is a bug; files not necessarily \n terminated */ if (*(V->buf) == '\0' && feof(V->f)) done = TRUE; done |= (*endTest)(V->buf, &addend); if (addend || !done) addseq(V->buf, V); } while (!done); } static int endPIR(char *s, int *addend) { *addend = 0; if ((strncmp(s, "///", 3) == 0) || (strncmp(s, "ENTRY", 5) == 0)) return 1; else return 0; } static void readPIR(struct ReadSeqVars *V) { char *sptr; /* load first line of entry */ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) { SeqfileGetLine(V); } if (feof(V->f)) return; if (V->ssimode >= 0) V->r_off = V->ssioffset; if ((sptr = strtok(V->buf + 15, "\n\t ")) != NULL) { SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); } do { SeqfileGetLine(V); if (!feof(V->f) && strncmp(V->buf, "TITLE", 5) == 0) SetSeqinfoString(V->sqinfo, V->buf+15, SQINFO_DESC); else if (!feof(V->f) && strncmp(V->buf, "ACCESSION", 9) == 0) { if ((sptr = strtok(V->buf+15, " \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); } } while (! feof(V->f) && (strncmp(V->buf,"SEQUENCE", 8) != 0)); SeqfileGetLine(V); /* skip next line, coords */ readLoop(0, endPIR, V); /* reading a real PIR-CODATA database file, we keep the source coords */ V->sqinfo->start = 1; V->sqinfo->stop = V->seqlen; V->sqinfo->olen = V->seqlen; V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN; /* get next line */ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) { SeqfileGetLine(V); } } static int endIG(char *s, int *addend) { *addend = 1; /* 1 or 2 occur in line w/ bases */ return((strchr(s,'1')!=NULL) || (strchr(s,'2')!=NULL)); } static void readIG(struct ReadSeqVars *V) { char *nm; /* position past ';' comments */ do { SeqfileGetLine(V); } while (! (feof(V->f) || ((*V->buf != 0) && (*V->buf != ';')) )); if (!feof(V->f)) { if ((nm = strtok(V->buf, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); readLoop(0, endIG, V); } while (!(feof(V->f) || ((*V->buf != '\0') && (*V->buf == ';')))) SeqfileGetLine(V); } static int endStrider(char *s, int *addend) { *addend = 0; return (strstr( s, "//") != NULL); } static void readStrider(struct ReadSeqVars *V) { char *nm; while ((!feof(V->f)) && (*V->buf == ';')) { if (strncmp(V->buf,"; DNA sequence", 14) == 0) { if ((nm = strtok(V->buf+16, ",\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); } SeqfileGetLine(V); } if (! feof(V->f)) readLoop(1, endStrider, V); /* load next line */ while ((!feof(V->f)) && (*V->buf != ';')) SeqfileGetLine(V); } static int endGB(char *s, int *addend) { *addend = 0; return ((strstr(s,"//") != NULL) || (strstr(s,"LOCUS") == s)); } static void readGenBank(struct ReadSeqVars *V) { char *sptr; int in_definition; /* We'll map three genbank identifiers onto names: * LOCUS -> sqinfo.name * ACCESSION -> sqinfo.acc [primary accession only] * VERSION -> sqinfo.id * We don't currently store the GI number, or secondary accessions. */ while (strncmp(V->buf, "LOCUS", 5) != 0) { SeqfileGetLine(V); } if (V->ssimode >= 0) V->r_off = V->ssioffset; if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); in_definition = FALSE; while (! feof(V->f)) { SeqfileGetLine(V); if (! feof(V->f) && strstr(V->buf, "DEFINITION") == V->buf) { if ((sptr = strtok(V->buf+12, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); in_definition = TRUE; } else if (! feof(V->f) && strstr(V->buf, "ACCESSION") == V->buf) { if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); in_definition = FALSE; } else if (! feof(V->f) && strstr(V->buf, "VERSION") == V->buf) { if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); in_definition = FALSE; } else if (strncmp(V->buf,"ORIGIN", 6) != 0) { if (in_definition) SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC); } else break; } readLoop(0, endGB, V); /* reading a real GenBank database file, we keep the source coords */ V->sqinfo->start = 1; V->sqinfo->stop = V->seqlen; V->sqinfo->olen = V->seqlen; V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN; while (!(feof(V->f) || ((*V->buf!=0) && (strstr(V->buf,"LOCUS") == V->buf)))) SeqfileGetLine(V); /* SRE: V->s now holds "//", so sequential reads are wedged: fixed Tue Jul 13 1993 */ while (!feof(V->f) && strstr(V->buf, "LOCUS ") != V->buf) SeqfileGetLine(V); } static int endGCGdata(char *s, int *addend) { *addend = 0; return (*s == '>'); } static void readGCGdata(struct ReadSeqVars *V) { int binary = FALSE; /* whether data are binary or not */ int blen = 0; /* length of binary sequence */ /* first line contains ">>>>" followed by name */ if (Strparse(">>>>([^ ]+) .+2BIT +Len: ([0-9]+)", V->buf, 2)) { binary = TRUE; SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME); blen = atoi(sqd_parse[2]); } else if (Strparse(">>>>([^ ]+) .+ASCII +Len: [0-9]+", V->buf, 1)) SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME); else Die("bogus GCGdata format? %s", V->buf); /* second line contains free text description */ SeqfileGetLine(V); SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC); if (binary) { /* allocate for blen characters +3... (allow for 3 bytes of slop) */ if (blen >= V->maxseq) { V->maxseq = blen; if ((V->seq = (char *) realloc (V->seq, sizeof(char)*(V->maxseq+4)))==NULL) Die("malloc failed"); } /* read (blen+3)/4 bytes from file */ if (fread(V->seq, sizeof(char), (blen+3)/4, V->f) < (size_t) ((blen+3)/4)) Die("fread failed"); V->seqlen = blen; /* convert binary code to seq */ GCGBinaryToSequence(V->seq, blen); } else readLoop(0, endGCGdata, V); while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>')))) SeqfileGetLine(V); } static int endPearson(char *s, int *addend) { *addend = 0; return(*s == '>'); } static void readPearson(struct ReadSeqVars *V) { char *sptr; if (V->ssimode >= 0) V->r_off = V->ssioffset; if (*V->buf != '>') Die("\ File %s does not appear to be in FASTA format at line %d.\n\ You may want to specify the file format on the command line.\n\ Usually this is done with an option --informat <fmt>.\n", V->fname, V->linenumber); if ((sptr = strtok(V->buf+1, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); if ((sptr = strtok(NULL, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); readLoop(0, endPearson, V); while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>')))) { SeqfileGetLine(V); } } static int endEMBL(char *s, int *addend) { *addend = 0; /* Some people (Berlin 5S rRNA database, f'r instance) use * an extended EMBL format that attaches extra data after * the sequence -- watch out for that. We use the fact that * real EMBL sequence lines begin with five spaces. * * We can use this as the sole end test because readEMBL() will * advance to the next ID line before starting to read again. */ return (strncmp(s," ",5) != 0); /* return ((strstr(s,"//") != NULL) || (strstr(s,"ID ") == s)); */ } static void readEMBL(struct ReadSeqVars *V) { char *sptr; /* make sure we have first line */ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) { SeqfileGetLine(V); } if (V->ssimode >= 0) V->r_off = V->ssioffset; if ((sptr = strtok(V->buf+5, "\n\t ")) != NULL) { SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); } do { SeqfileGetLine(V); if (!feof(V->f) && strstr(V->buf, "AC ") == V->buf) { if ((sptr = strtok(V->buf+5, "; \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); } else if (!feof(V->f) && strstr(V->buf, "DE ") == V->buf) { if ((sptr = strtok(V->buf+5, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); } } while (! feof(V->f) && strncmp(V->buf,"SQ",2) != 0); readLoop(0, endEMBL, V); /* Hack for Staden experiment files: convert - to N */ if (V->ssimode == -1) /* if we're in ssi mode, we're not keeping the seq */ for (sptr = V->seq; *sptr != '\0'; sptr++) if (*sptr == '-') *sptr = 'N'; /* reading a real EMBL database file, we keep the source coords */ V->sqinfo->start = 1; V->sqinfo->stop = V->seqlen; V->sqinfo->olen = V->seqlen; V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN; /* load next record's ID line */ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) { SeqfileGetLine(V); } } static int endZuker(char *s, int *addend) { *addend = 0; return( *s == '(' ); } static void readZuker(struct ReadSeqVars *V) { char *sptr; SeqfileGetLine(V); /*s == "seqLen seqid string..."*/ if ((sptr = strtok(V->buf+6, " \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); if ((sptr = strtok(NULL, "\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); readLoop(0, endZuker, V); while (!(feof(V->f) | ((*V->buf != '\0') & (*V->buf == '(')))) SeqfileGetLine(V); } static void readUWGCG(struct ReadSeqVars *V) { char *si; char *sptr; int done; V->seqlen = 0; /*writeseq: " %s Length: %d (today) Check: %d ..\n" */ /*drop above or ".." from id*/ if ((si = strstr(V->buf," Length: ")) != NULL) *si = 0; else if ((si = strstr(V->buf,"..")) != NULL) *si = 0; if ((sptr = strtok(V->buf, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); do { done = feof(V->f); SeqfileGetLine(V); if (! done) addseq(V->buf, V); } while (!done); } /* Function: ReadSeq() * * Purpose: Read next sequence from an open database file. * Return the sequence and associated info. * * Args: fp - open sequence database file pointer * format - format of the file (previously determined * by call to SeqfileFormat()). * Currently unused, since we carry it in V. * ret_seq - RETURN: sequence * sqinfo - RETURN: filled in w/ other information * * Limitations: uses squid_errno, so it's not threadsafe. * * Return: 1 on success, 0 on failure. * ret_seq and some field of sqinfo are allocated here, * The preferred call mechanism to properly free the memory is: * * SQINFO sqinfo; * char *seq; * * ReadSeq(fp, format, &seq, &sqinfo); * ... do something... * FreeSequence(seq, &sqinfo); */ int ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) { int gotuw; squid_errno = SQERR_OK; /* Here's the hack for sequential access of sequences from * the multiple sequence alignment formats */ if (IsAlignmentFormat(V->format)) { if (V->msa->lastidx >= V->msa->nseq) { /* out of data. try to read another alignment */ MSAFree(V->msa); if ((V->msa = MSAFileRead(V->afp)) == NULL) return 0; V->msa->lastidx = 0; } /* copy and dealign the appropriate aligned seq */ /* AW: stopping squid from dealigning sequences and corresponding info */ #ifdef CLUSTALO V->seq = sre_strdup(V->msa->aseq[V->msa->lastidx], V->msa->alen); #else MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen, V->msa->aseq[V->msa->lastidx], &(V->seq)); #endif V->seqlen = strlen(V->seq); /* Extract sqinfo stuff for this sequence from the msa. * Tedious; code that should be cleaned. */ sqinfo->flags = 0; if (V->msa->sqname[V->msa->lastidx] != NULL) SetSeqinfoString(sqinfo, V->msa->sqname[V->msa->lastidx], SQINFO_NAME); if (V->msa->sqacc != NULL && V->msa->sqacc[V->msa->lastidx] != NULL) SetSeqinfoString(sqinfo, V->msa->sqacc[V->msa->lastidx], SQINFO_ACC); if (V->msa->sqdesc != NULL && V->msa->sqdesc[V->msa->lastidx] != NULL) SetSeqinfoString(sqinfo, V->msa->sqdesc[V->msa->lastidx], SQINFO_DESC); if (V->msa->ss != NULL && V->msa->ss[V->msa->lastidx] != NULL) { /* AW: stopping squid from dealigning sequences and corresponding info */ #ifdef CLUSTALO sqinfo->ss = sre_strdup(V->msa->ss[V->msa->lastidx], V->msa->alen); #else MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen, V->msa->ss[V->msa->lastidx], &(sqinfo->ss)); #endif sqinfo->flags |= SQINFO_SS; } if (V->msa->sa != NULL && V->msa->sa[V->msa->lastidx] != NULL) { /* AW: stopping squid from dealigning sequences and corresponding info */ #ifdef CLUSTALO sqinfo->sa = sre_strdup(V->msa->sa[V->msa->lastidx], V->msa->alen); #else MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen, V->msa->sa[V->msa->lastidx], &(sqinfo->sa)); #endif sqinfo->flags |= SQINFO_SA; } V->msa->lastidx++; } else { if (feof(V->f)) return 0; if (V->ssimode == -1) { /* normal mode */ V->seq = (char*) calloc (kStartLength+1, sizeof(char)); V->maxseq = kStartLength; } else { /* index mode: discarding seq */ V->seq = NULL; V->maxseq = 0; } V->seqlen = 0; V->sqinfo = sqinfo; V->sqinfo->flags = 0; switch (V->format) { case SQFILE_IG : readIG(V); break; case SQFILE_STRIDER : readStrider(V); break; case SQFILE_GENBANK : readGenBank(V); break; case SQFILE_FASTA : readPearson(V); break; case SQFILE_EMBL : readEMBL(V); break; case SQFILE_ZUKER : readZuker(V); break; case SQFILE_PIR : readPIR(V); break; case SQFILE_GCGDATA : readGCGdata(V); break; case SQFILE_GCG : do { /* skip leading comments on GCG file */ gotuw = (strstr(V->buf,"..") != NULL); if (gotuw) readUWGCG(V); SeqfileGetLine(V); } while (! feof(V->f)); break; case SQFILE_IDRAW: /* SRE: no attempt to read idraw postscript */ default: squid_errno = SQERR_FORMAT; free(V->seq); return 0; } if (V->seq != NULL) /* (it can be NULL in indexing mode) */ V->seq[V->seqlen] = 0; /* stick a string terminator on it */ } /* Cleanup */ sqinfo->len = V->seqlen; sqinfo->flags |= SQINFO_LEN; *ret_seq = V->seq; if (squid_errno == SQERR_OK) return 1; else return 0; } /* Function: SeqfileFormat() * Date: SRE, Tue Jun 22 10:58:58 1999 [Sanger Centre] * * Purpose: Determine format of an open file. * Returns format code. * Rewinds the file. * * Autodetects the following unaligned formats: * SQFILE_FASTA * SQFILE_GENBANK * SQFILE_EMBL * SQFILE_GCG * SQFILE_GCGDATA * SQFILE_PIR * Also autodetects the following alignment formats: * MSAFILE_STOCKHOLM * MSAFILE_MSF * MSAFILE_CLUSTAL * MSAFILE_SELEX * MSAFILE_PHYLIP * * Can't autodetect MSAFILE_A2M, calls it SQFILE_FASTA. * MSAFileFormat() does the opposite. * * Args: sfp - open SQFILE * * Return: format code, or SQFILE_UNKNOWN if unrecognized */ int SeqfileFormat(FILE *fp) { char *buf; int len; int fmt = SQFILE_UNKNOWN; int ndataline; char *bufcpy, *s, *s1, *s2; int has_junk; buf = NULL; len = 0; ndataline = 0; has_junk = FALSE; while (sre_fgets(&buf, &len, fp) != NULL) { if (IsBlankline(buf)) continue; /* Well-behaved formats identify themselves in first nonblank line. */ if (ndataline == 0) { if (strncmp(buf, ">>>>", 4) == 0 && strstr(buf, "Len: ")) { fmt = SQFILE_GCGDATA; goto DONE; } if (buf[0] == '>') { fmt = SQFILE_FASTA; goto DONE; } if (strncmp(buf, "!!AA_SEQUENCE", 13) == 0 || strncmp(buf, "!!NA_SEQUENCE", 13) == 0) { fmt = SQFILE_GCG; goto DONE; } if (strncmp(buf, "# STOCKHOLM 1.", 14) == 0) { fmt = MSAFILE_STOCKHOLM; goto DONE; } if (strncmp(buf, "CLUSTAL", 7) == 0 && strstr(buf, "multiple sequence alignment") != NULL) { fmt = MSAFILE_CLUSTAL; goto DONE; } if (strncmp(buf, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0 || strncmp(buf, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0) { fmt = MSAFILE_MSF; goto DONE; } /* PHYLIP id: also just a good bet */ bufcpy = sre_strdup(buf, -1); s = bufcpy; if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) != NULL && (s2 = sre_strtok(&s, WHITESPACE, NULL)) != NULL && IsInt(s1) && IsInt(s2)) { free(bufcpy); fmt = MSAFILE_PHYLIP; goto DONE; } free(bufcpy); } /* We trust that other formats identify themselves soon. */ /* dead giveaways for extended SELEX */ if (strncmp(buf, "#=AU", 4) == 0 || strncmp(buf, "#=ID", 4) == 0 || strncmp(buf, "#=AC", 4) == 0 || strncmp(buf, "#=DE", 4) == 0 || strncmp(buf, "#=GA", 4) == 0 || strncmp(buf, "#=TC", 4) == 0 || strncmp(buf, "#=NC", 4) == 0 || strncmp(buf, "#=SQ", 4) == 0 || strncmp(buf, "#=SS", 4) == 0 || strncmp(buf, "#=CS", 4) == 0 || strncmp(buf, "#=RF", 4) == 0) { fmt = MSAFILE_SELEX; goto DONE; } if (strncmp(buf, "///", 3) == 0 || strncmp(buf, "ENTRY ", 6) == 0) { fmt = SQFILE_PIR; goto DONE; } /* a ha, diagnostic of an (old) MSF file */ if ((strstr(buf, "..") != NULL) && (strstr(buf, "MSF:") != NULL) && (strstr(buf, "Check:")!= NULL)) { fmt = MSAFILE_MSF; goto DONE; } /* unaligned GCG (must follow MSF test!) */ if (strstr(buf, " Check: ") != NULL && strstr(buf, "..") != NULL) { fmt = SQFILE_GCG; goto DONE; } if (strncmp(buf,"LOCUS ",6) == 0 || strncmp(buf,"ORIGIN ",6) == 0) { fmt = SQFILE_GENBANK; goto DONE; } if (strncmp(buf,"ID ",5) == 0 || strncmp(buf,"SQ ",5) == 0) { fmt = SQFILE_EMBL; goto DONE; } /* But past here, we're being desperate. A simple SELEX file is * very difficult to detect; we can only try to disprove it. */ s = buf; if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; /* skip blank lines */ if (strchr("#%", *s1) != NULL) continue; /* skip comment lines */ /* Disproof 1. Noncomment, nonblank lines in a SELEX file * must have at least two space-delimited fields (name/seq) */ if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) has_junk = TRUE; /* Disproof 2. * The sequence field should look like a sequence. */ if (s2 != NULL && Seqtype(s2) == kOtherSeq) has_junk = TRUE; ndataline++; if (ndataline == 300) break; /* only look at first 300 lines */ } if (ndataline == 0) Die("Sequence file contains no data"); /* If we've made it this far, we've run out of data, but there * was at least one line of it; check if we've * disproven SELEX. If not, cross our fingers, pray, and guess SELEX. */ if (has_junk == TRUE) fmt = SQFILE_UNKNOWN; else fmt = MSAFILE_SELEX; DONE: if (buf != NULL) free(buf); rewind(fp); return fmt; } /* Function: GCGBinaryToSequence() * * Purpose: Convert a GCG 2BIT binary string to DNA sequence. * 0 = C 1 = T 2 = A 3 = G * 4 nts/byte * * Args: seq - binary sequence. Converted in place to DNA. * len - length of DNA. binary is (len+3)/4 bytes */ int GCGBinaryToSequence(char *seq, int len) { int bpos; /* position in binary */ int spos; /* position in sequence */ char twobit; int i; for (bpos = (len-1)/4; bpos >= 0; bpos--) { twobit = seq[bpos]; spos = bpos*4; for (i = 3; i >= 0; i--) { switch (twobit & 0x3) { case 0: seq[spos+i] = 'C'; break; case 1: seq[spos+i] = 'T'; break; case 2: seq[spos+i] = 'A'; break; case 3: seq[spos+i] = 'G'; break; } twobit = twobit >> 2; } } seq[len] = '\0'; return 1; } /* Function: GCGchecksum() * Date: SRE, Mon May 31 11:13:21 1999 [St. Louis] * * Purpose: Calculate a GCG checksum for a sequence. * Code provided by Steve Smith of Genetics * Computer Group. * * Args: seq - sequence to calculate checksum for. * may contain gap symbols. * len - length of sequence (usually known, * so save a strlen() call) * * Returns: GCG checksum. */ int GCGchecksum(char *seq, int len) { int i; /* position in sequence */ int chk = 0; /* calculated checksum */ for (i = 0; i < len; i++) chk = (chk + (i % 57 + 1) * (sre_toupper((int) seq[i]))) % 10000; return chk; } /* Function: GCGMultchecksum() * * Purpose: GCG checksum for a multiple alignment: sum of * individual sequence checksums (including their * gap characters) modulo 10000. * * Implemented using spec provided by Steve Smith of * Genetics Computer Group. * * Args: seqs - sequences to be checksummed; aligned or not * nseq - number of sequences * * Return: the checksum, a number between 0 and 9999 */ int GCGMultchecksum(char **seqs, int nseq) { int chk = 0; int idx; for (idx = 0; idx < nseq; idx++) chk = (chk + GCGchecksum(seqs[idx], strlen(seqs[idx]))) % 10000; return chk; } /* Function: Seqtype() * * Purpose: Returns a (very good) guess about type of sequence: * kDNA, kRNA, kAmino, or kOtherSeq. * * Modified from, and replaces, Gilbert getseqtype(). */ int Seqtype(char *seq) { int saw; /* how many non-gap characters I saw */ char c; int po = 0; /* count of protein-only */ int nt = 0; /* count of t's */ int nu = 0; /* count of u's */ int na = 0; /* count of nucleotides */ int aa = 0; /* count of amino acids */ int no = 0; /* count of others */ /* Look at the first 300 non-gap characters */ #ifdef CLUSTALO /* VGGNGDDYLSGGTGNDTL is recognized as unknown using squid's default * approach. * We change it to the following: * 1. counting: ignore gaps and not alpha characters. if protein-only then * count as such (po). otherwise decide if amino-acid (aa) or nucleic-acid * (na) or unknown (no) * * 2. determine type: if we saw more unknown than aa or na, return unknown. * if encountered protein-only return protein-only. otherwise decide based * on majority. (if aa==na return na) */ for (saw = 0; *seq != '\0' && saw < 300; seq++) { c = sre_toupper((int) *seq); int unknown = 1; if (isgap(c) || ! isalpha((int) c)) { continue; } if (strchr(protonly, c)) { po++; unknown = 0; } if (strchr(aminos,c)) { aa++; unknown = 0; } if (strchr(primenuc,c)) { na++; unknown = 0; if (c == 'T') nt++; else if (c == 'U') nu++; } if (unknown) { no ++; } saw++; } if (no > aa && no > na) return kOtherSeq; if (po > 0 || aa>na) return kAmino; if (na >= aa) { if (nu > nt) return kRNA; else return kDNA; } return kOtherSeq; #else for (saw = 0; *seq != '\0' && saw < 300; seq++) { c = sre_toupper((int) *seq); if (! isgap(c)) { if (strchr(protonly, c)) po++; else if (strchr(primenuc,c)) { na++; if (c == 'T') nt++; else if (c == 'U') nu++; } else if (strchr(aminos,c)) aa++; else if (isalpha((int) c)) no++; saw++; } } if (no > 0) return kOtherSeq; else if (po > 0) return kAmino; else if (na > aa) { if (nu > nt) return kRNA; else return kDNA; } else return kAmino; /* ooooh. risky. */ #endif } /* Function: GuessAlignmentSeqtype() * Date: SRE, Wed Jul 7 09:42:34 1999 [St. Louis] * * Purpose: Try to guess whether an alignment is protein * or nucleic acid; return a code for the * type (kRNA, kDNA, or kAmino). * * Args: aseq - array of aligned sequences. (Could also * be an rseq unaligned sequence array) * nseq - number of aseqs * * Returns: kRNA, kDNA, kAmino; * kOtherSeq if inconsistency is detected. */ int GuessAlignmentSeqtype(char **aseq, int nseq) { int idx; int nrna = 0; int ndna = 0; int namino = 0; int nother = 0; for (idx = 0; idx < nseq; idx++) switch (Seqtype(aseq[idx])) { case kRNA: nrna++; break; case kDNA: ndna++; break; case kAmino: namino++; break; default: nother++; } /* Unambiguous decisions: */ if (nother) return kOtherSeq; if (namino == nseq) return kAmino; if (ndna == nseq) return kDNA; if (nrna == nseq) return kRNA; /* Ambiguous decisions: */ if (namino == 0) return kRNA; /* it's nucleic acid, but seems mixed RNA/DNA */ return kAmino; /* some amino acid seen; others probably short seqs, some of which may be entirely ACGT (ala,cys,gly,thr). We could be a little more sophisticated: U would be a giveaway that we're not in protein seqs */ } /* Function: WriteSimpleFASTA() * Date: SRE, Tue Nov 16 18:06:00 1999 [St. Louis] * * Purpose: Just write a FASTA format sequence to a file; * minimal interface, mostly for quick and dirty programs. * * Args: fp - open file handle (stdout, possibly) * seq - sequence to output * name - name for the sequence * desc - optional description line, or NULL. * * Returns: void */ void WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc) { char buf[61]; int len; int pos; len = strlen(seq); buf[60] = '\0'; fprintf(fp, ">%s %s\n", name, desc != NULL ? desc : ""); for (pos = 0; pos < len; pos += 60) { strncpy(buf, seq+pos, 60); fprintf(fp, "%s\n", buf); } } int WriteSeq(FILE *outf, int outform, char *seq, SQINFO *sqinfo) { int numline = 0; int lines = 0, spacer = 0, width = 50, tab = 0; int i, j, l, l1, ibase; char endstr[10]; char s[100]; /* buffer for sequence */ char ss[100]; /* buffer for structure */ int checksum = 0; int seqlen; int which_case; /* 0 = do nothing. 1 = upper case. 2 = lower case */ int dostruc; /* TRUE to print structure lines*/ which_case = 0; dostruc = FALSE; seqlen = (sqinfo->flags & SQINFO_LEN) ? sqinfo->len : strlen(seq); if (IsAlignmentFormat(outform)) Die("Tried to write an aligned format with WriteSeq() -- bad, bad."); strcpy( endstr,""); l1 = 0; checksum = GCGchecksum(seq, seqlen); switch (outform) { case SQFILE_UNKNOWN: /* no header, just sequence */ strcpy(endstr,"\n"); /* end w/ extra blank line */ break; case SQFILE_GENBANK: fprintf(outf,"LOCUS %s %d bp\n", sqinfo->name, seqlen); fprintf(outf,"ACCESSION %s\n", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "."); fprintf(outf,"DEFINITION %s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "."); fprintf(outf,"VERSION %s\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : "."); fprintf(outf,"ORIGIN \n"); spacer = 11; numline = 1; strcpy(endstr, "\n//"); break; case SQFILE_GCGDATA: fprintf(outf, ">>>>%s 9/95 ASCII Len: %d\n", sqinfo->name, seqlen); fprintf(outf, "%s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-"); break; case SQFILE_PIR: fprintf(outf, "ENTRY %s\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name); fprintf(outf, "TITLE %s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-"); fprintf(outf, "ACCESSION %s\n", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-"); fprintf(outf, "SUMMARY #Length %d #Checksum %d\n", sqinfo->len, checksum); fprintf(outf, "SEQUENCE\n"); fprintf(outf, " 5 10 15 20 25 30\n"); spacer = 2; /* spaces after every residue */ numline = 1; /* number lines w/ coords */ width = 30; /* 30 aa per line */ strcpy(endstr, "\n///"); break; case SQFILE_SQUID: fprintf(outf, "NAM %s\n", sqinfo->name); if (sqinfo->flags & (SQINFO_ID | SQINFO_ACC | SQINFO_START | SQINFO_STOP | SQINFO_OLEN)) fprintf(outf, "SRC %s %s %d..%d::%d\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : "-", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-", (sqinfo->flags & SQINFO_START) ? sqinfo->start : 0, (sqinfo->flags & SQINFO_STOP) ? sqinfo->stop : 0, (sqinfo->flags & SQINFO_OLEN) ? sqinfo->olen : 0); if (sqinfo->flags & SQINFO_DESC) fprintf(outf, "DES %s\n", sqinfo->desc); if (sqinfo->flags & SQINFO_SS) { fprintf(outf, "SEQ +SS\n"); dostruc = TRUE; /* print structure lines too */ } else fprintf(outf, "SEQ\n"); numline = 1; /* number seq lines w/ coords */ strcpy(endstr, "\n++"); break; case SQFILE_EMBL: fprintf(outf,"ID %s\n", (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name); fprintf(outf,"AC %s\n", (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-"); fprintf(outf,"DE %s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-"); fprintf(outf,"SQ %d BP\n", seqlen); strcpy(endstr, "\n//"); /* 11Oct90: bug fix*/ tab = 5; /** added 31jan91 */ spacer = 11; /** added 31jan91 */ break; case SQFILE_GCG: fprintf(outf,"%s\n", sqinfo->name); if (sqinfo->flags & SQINFO_ACC) fprintf(outf,"ACCESSION %s\n", sqinfo->acc); if (sqinfo->flags & SQINFO_DESC) fprintf(outf,"DEFINITION %s\n", sqinfo->desc); fprintf(outf," %s Length: %d (today) Check: %d ..\n", sqinfo->name, seqlen, checksum); spacer = 11; numline = 1; strcpy(endstr, "\n"); /* this is insurance to help prevent misreads at eof */ break; case SQFILE_STRIDER: /* ?? map ?*/ fprintf(outf,"; ### from DNA Strider ;-)\n"); fprintf(outf,"; DNA sequence %s, %d bases, %d checksum.\n;\n", sqinfo->name, seqlen, checksum); strcpy(endstr, "\n//"); break; /* SRE: Don had Zuker default to Pearson, which is not intuitive or helpful, since Zuker's MFOLD can't read Pearson format. More useful to use kIG */ case SQFILE_ZUKER: which_case = 1; /* MFOLD requires upper case. */ /*FALLTHRU*/ case SQFILE_IG: fprintf(outf,";%s %s\n", sqinfo->name, (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : ""); fprintf(outf,"%s\n", sqinfo->name); strcpy(endstr,"1"); /* == linear dna */ break; case SQFILE_RAW: /* Raw: no header at all. */ break; default : case SQFILE_FASTA: fprintf(outf,">%s %s\n", sqinfo->name, (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : ""); break; } if (which_case == 1) s2upper(seq); if (which_case == 2) s2lower(seq); width = MIN(width,100); for (i=0, l=0, ibase = 1, lines = 0; i < seqlen; ) { if (l1 < 0) l1 = 0; else if (l1 == 0) { if (numline) fprintf(outf,"%8d ",ibase); for (j=0; j<tab; j++) fputc(' ',outf); } if ((spacer != 0) && ((l+1) % spacer == 1)) { s[l] = ' '; ss[l] = ' '; l++; } s[l] = seq[i]; ss[l] = (sqinfo->flags & SQINFO_SS) ? sqinfo->ss[i] : '.'; l++; i++; l1++; /* don't count spaces for width*/ if (l1 == width || i == seqlen) { s[l] = ss[l] = '\0'; l = 0; l1 = 0; if (dostruc) { fprintf(outf, "%s\n", s); if (numline) fprintf(outf," "); for (j=0; j<tab; j++) fputc(' ',outf); if (i == seqlen) fprintf(outf,"%s%s\n",ss,endstr); else fprintf(outf,"%s\n",ss); } else { if (i == seqlen) fprintf(outf,"%s%s\n",s,endstr); else fprintf(outf,"%s\n",s); } lines++; ibase = i+1; } } return lines; } /* Function: ReadMultipleRseqs() * * Purpose: Open a data file and * parse it into an array of rseqs (raw, unaligned * sequences). * * Caller is responsible for free'ing memory allocated * to ret_rseqs, ret_weights, and ret_names. * * Weights are currently only supported for MSF format. * Sequences read from all other formats will be assigned * weights of 1.0. If the caller isn't interested in * weights, it passes NULL as ret_weights. * * Returns 1 on success. Returns 0 on failure and sets * squid_errno to indicate the cause. */ int ReadMultipleRseqs(char *seqfile, int fformat, char ***ret_rseqs, SQINFO **ret_sqinfo, int *ret_num) { SQINFO *sqinfo; /* array of sequence optional info */ SQFILE *dbfp; /* open ptr for sequential access of file */ char **rseqs; /* sequence array */ int numalloced; /* num of seqs currently alloced for */ int num; num = 0; numalloced = 16; rseqs = (char **) MallocOrDie (numalloced * sizeof(char *)); sqinfo = (SQINFO *) MallocOrDie (numalloced * sizeof(SQINFO)); if ((dbfp = SeqfileOpen(seqfile, fformat, NULL)) == NULL) return 0; while (ReadSeq(dbfp, dbfp->format, &rseqs[num], &(sqinfo[num]))) { num++; if (num == numalloced) /* more seqs coming, alloc more room */ { numalloced += 16; rseqs = (char **) ReallocOrDie (rseqs, numalloced*sizeof(char *)); sqinfo = (SQINFO *) ReallocOrDie (sqinfo, numalloced * sizeof(SQINFO)); } } SeqfileClose(dbfp); *ret_rseqs = rseqs; *ret_sqinfo = sqinfo; *ret_num = num; return 1; } /* Function: String2SeqfileFormat() * Date: SRE, Sun Jun 27 15:25:54 1999 [TW 723 over Canadian Shield] * * Purpose: Convert a string (e.g. from command line option arg) * to a format code. Case insensitive. Return * MSAFILE_UNKNOWN/SQFILE_UNKNOWN if string is bad. * Uses codes defined in squid.h (unaligned formats) and * msa.h (aligned formats). * * Args: s - string to convert; e.g. "stockholm" * * Returns: format code; e.g. MSAFILE_STOCKHOLM */ int String2SeqfileFormat(char *s) { char *s2; int code = SQFILE_UNKNOWN; if (s == NULL) return SQFILE_UNKNOWN; s2 = sre_strdup(s, -1); s2upper(s2); if (strcmp(s2, "FASTA") == 0) code = SQFILE_FASTA; #ifdef CLUSTALO if (strcmp(s2, "FA") == 0) code = SQFILE_FASTA; else if (strcmp(s2, "VIENNA") == 0) code = SQFILE_VIENNA; else if (strcmp(s2, "VIE") == 0) code = SQFILE_VIENNA; #endif else if (strcmp(s2, "GENBANK") == 0) code = SQFILE_GENBANK; #ifdef CLUSTALO else if (strcmp(s2, "GB") == 0) code = SQFILE_GENBANK; #endif else if (strcmp(s2, "EMBL") == 0) code = SQFILE_EMBL; else if (strcmp(s2, "GCG") == 0) code = SQFILE_GCG; else if (strcmp(s2, "GCGDATA") == 0) code = SQFILE_GCGDATA; else if (strcmp(s2, "RAW") == 0) code = SQFILE_RAW; else if (strcmp(s2, "IG") == 0) code = SQFILE_IG; else if (strcmp(s2, "STRIDER") == 0) code = SQFILE_STRIDER; else if (strcmp(s2, "IDRAW") == 0) code = SQFILE_IDRAW; else if (strcmp(s2, "ZUKER") == 0) code = SQFILE_ZUKER; else if (strcmp(s2, "PIR") == 0) code = SQFILE_PIR; else if (strcmp(s2, "SQUID") == 0) code = SQFILE_SQUID; else if (strcmp(s2, "STOCKHOLM") == 0) code = MSAFILE_STOCKHOLM; #ifdef CLUSTALO else if (strcmp(s2, "ST") == 0) code = MSAFILE_STOCKHOLM; else if (strcmp(s2, "STK") == 0) code = MSAFILE_STOCKHOLM; #endif else if (strcmp(s2, "SELEX") == 0) code = MSAFILE_SELEX; else if (strcmp(s2, "MSF") == 0) code = MSAFILE_MSF; else if (strcmp(s2, "CLUSTAL") == 0) code = MSAFILE_CLUSTAL; #ifdef CLUSTALO else if (strcmp(s2, "CLU") == 0) code = MSAFILE_CLUSTAL; #endif else if (strcmp(s2, "A2M") == 0) code = MSAFILE_A2M; else if (strcmp(s2, "PHYLIP") == 0) code = MSAFILE_PHYLIP; #ifdef CLUSTALO else if (strcmp(s2, "PHY") == 0) code = MSAFILE_PHYLIP; #endif else if (strcmp(s2, "EPS") == 0) code = MSAFILE_EPS; #ifdef CLUSTALO else code = SQFILE_UNKNOWN; #endif free(s2); return code; } char * SeqfileFormat2String(int code) { switch (code) { case SQFILE_UNKNOWN: return "unknown"; case SQFILE_FASTA: return "FASTA"; #ifdef CLUSTALO case SQFILE_VIENNA: return "Vienna"; #endif case SQFILE_GENBANK: return "Genbank"; case SQFILE_EMBL: return "EMBL"; case SQFILE_GCG: return "GCG"; case SQFILE_GCGDATA: return "GCG data library"; case SQFILE_RAW: return "raw"; case SQFILE_IG: return "Intelligenetics"; case SQFILE_STRIDER: return "MacStrider"; case SQFILE_IDRAW: return "Idraw Postscript"; case SQFILE_ZUKER: return "Zuker"; case SQFILE_PIR: return "PIR"; case SQFILE_SQUID: return "SQUID"; case MSAFILE_STOCKHOLM: return "Stockholm"; case MSAFILE_SELEX: return "SELEX"; case MSAFILE_MSF: return "MSF"; case MSAFILE_CLUSTAL: return "Clustal"; case MSAFILE_A2M: return "a2m"; case MSAFILE_PHYLIP: return "Phylip"; case MSAFILE_EPS: return "EPS"; default: Die("Bad code passed to MSAFormat2String()"); } /*NOTREACHED*/ return NULL; } /* Function: MSAToSqinfo() * Date: SRE, Tue Jul 20 14:36:56 1999 [St. Louis] * * Purpose: Take an MSA and generate a SQINFO array suitable * for use in annotating the unaligned sequences. * Return the array. * * Permanent temporary code. sqinfo was poorly designed. * it must eventually be replaced, but the odds * of this happening soon are nil, so I have to deal. * * Args: msa - the alignment * * Returns: ptr to allocated sqinfo array. * Freeing is ghastly: free in each individual sqinfo[i] * with FreeSequence(NULL, &(sqinfo[i])), then * free(sqinfo). */ SQINFO * MSAToSqinfo(MSA *msa) { int idx; SQINFO *sqinfo; sqinfo = MallocOrDie(sizeof(SQINFO) * msa->nseq); for (idx = 0; idx < msa->nseq; idx++) { sqinfo[idx].flags = 0; SetSeqinfoString(&(sqinfo[idx]), msa->sqname[idx], SQINFO_NAME); SetSeqinfoString(&(sqinfo[idx]), MSAGetSeqAccession(msa, idx), SQINFO_ACC); SetSeqinfoString(&(sqinfo[idx]), MSAGetSeqDescription(msa, idx), SQINFO_DESC); if (msa->ss != NULL && msa->ss[idx] != NULL) { MakeDealignedString(msa->aseq[idx], msa->alen, msa->ss[idx], &(sqinfo[idx].ss)); sqinfo[idx].flags |= SQINFO_SS; } if (msa->sa != NULL && msa->sa[idx] != NULL) { MakeDealignedString(msa->aseq[idx], msa->alen, msa->sa[idx], &(sqinfo[idx].sa)); sqinfo[idx].flags |= SQINFO_SA; } sqinfo[idx].len = DealignedLength(msa->aseq[idx]); sqinfo[idx].flags |= SQINFO_LEN; } return sqinfo; } /* cc -o sqio_test -DA_QUIET_DAY -L. sqio.c -lsquid */ #ifdef A_QUIET_DAY #include "ssi.h" int main(int argc, char **argv) { FILE *fp; char *filename; char *buf; int len; int mode = 3; SSIOFFSET off; filename = argv[1]; if (mode == 1) { buf = malloc(sizeof(char) * 256); if ((fp = fopen(filename, "r")) == NULL) Die("open of %s failed", filename); while (fgets(buf, 255, fp) != NULL) ; fclose(fp); free(buf); } else if (mode == 2) { if ((fp = fopen(filename, "r")) == NULL) Die("open of %s failed", filename); buf = NULL; len = 0; while (sre_fgets(&buf, &len, fp) != NULL) SSIGetFilePosition(fp, SSI_OFFSET_I32, &off); fclose(fp); free(buf); } else if (mode == 3) { SQFILE *dbfp; SQINFO info; if ((dbfp = SeqfileOpen(filename, SQFILE_FASTA, NULL)) == NULL) Die("open of %s failed", filename); while (ReadSeq(dbfp, dbfp->format, &buf, &info)) { SSIGetFilePosition(dbfp->f, SSI_OFFSET_I32, &off); FreeSequence(buf, &info); } SeqfileClose(dbfp); } } #endif