Mercurial > repos > clustalomega > clustalomega
diff clustalomega/clustal-omega-1.0.2/src/squid/a2m.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustalomega/clustal-omega-1.0.2/src/squid/a2m.c Thu Jul 21 13:35:08 2011 -0400 @@ -0,0 +1,134 @@ +/***************************************************************** + * 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. + *****************************************************************/ + +/* a2m.c + * + * reading/writing A2M (aligned FASTA) files. + * + * RCS $Id: a2m.c 242 2011-05-27 14:04:21Z andreas $ (Original squid RCS Id: a2m.c,v 1.1 1999/07/15 22:26:40 eddy Exp) + */ + +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include "squid.h" +#include "msa.h" + +/* Function: ReadA2M() + * Date: SRE, Sun Jun 6 17:11:29 1999 [bus from Madison 1999 worm mtg] + * + * Purpose: Parse an alignment read from an open A2M format + * alignment file. A2M is a single alignment format. + * Return the alignment, or NULL if we've already + * read the alignment. + * + * Args: afp - open alignment file + * + * Returns: MSA * - an alignment object. + * Caller responsible for an MSAFree() + */ +MSA * +ReadA2M(MSAFILE *afp) +{ + MSA *msa; + char *buf; + char *name; + char *desc; + char *seq; + int idx; + int len1, len2; + + if (feof(afp->f)) return NULL; + + name = NULL; + msa = MSAAlloc(10, 0); + idx = 0; + while ((buf = MSAFileGetLine(afp)) != NULL) + { + if (*buf == '>') + { + buf++; /* skip the '>' */ + if ((name = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) + Die("Blank name in A2M file %s (line %d)\n", afp->fname, afp->linenumber); + desc = sre_strtok(&buf, "\n", &len2); + + idx = GKIStoreKey(msa->index, name); + if (idx >= msa->nseqalloc) MSAExpand(msa); + + msa->sqname[idx] = sre_strdup(name, len1); + if (desc != NULL) MSASetSeqDescription(msa, idx, desc); + msa->nseq++; + } + else if (name != NULL) + { + if ((seq = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) continue; + msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], seq, len1); + } + } + if (name == NULL) { MSAFree(msa); return NULL; } + + MSAVerifyParse(msa); + return msa; +} + + +/* Function: WriteA2M() + * Date: SRE, Sun Jun 6 17:40:35 1999 [bus from Madison, 1999 worm mtg] + * + * Purpose: Write an "aligned FASTA" (aka a2m, to UCSC) formatted + * alignment. + * + * Args: fp - open FILE to write to. + * msa - alignment to write + * + * Returns: void + */ +void +#ifdef CLUSTALO +WriteA2M(FILE *fp, MSA *msa, int vienna) +#else +WriteA2M(FILE *fp, MSA *msa) +#endif +{ + int idx; /* sequence index */ + int pos; /* position in sequence */ + char buf[64]; /* buffer for individual lines */ + int cpl = 60; /* char per line; must be < 64 unless buf is bigger */ + + buf[cpl] = '\0'; + for (idx = 0; idx < msa->nseq; idx++) + { +#ifdef CLUSTALO + /* most fasta sequences don't have a description, which + * leads to a trailing white space in the original code + */ + fprintf(fp, ">%s", msa->sqname[idx]); + + if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL && !vienna) { + fprintf(fp, " %s", msa->sqdesc[idx]); + } + fprintf(fp, "\n"); +#else + fprintf(fp, ">%s %s\n", + msa->sqname[idx], + (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) ? msa->sqdesc[idx] : ""); +#endif + for (pos = 0; pos < msa->alen; pos+=cpl) + { + strncpy(buf, &(msa->aseq[idx][pos]), cpl); + if (vienna) + fprintf(fp, "%s", buf); + else + fprintf(fp, "%s\n", buf); + } + if (vienna) + fprintf(fp, "\n"); + + } +}