1 /*****************************************************************
2 * SQUID - a library of functions for biological sequence analysis
3 * Copyright (C) 1992-2002 Washington University School of Medicine
4 *
5 * This source code is freely distributed under the terms of the
6 * GNU General Public License. See the files COPYRIGHT and LICENSE
7 * for details.
8 *****************************************************************/
9
10 /* a2m.c
11 *
12 * reading/writing A2M (aligned FASTA) files.
13 *
14 * RCS $Id: a2m.c 297 2014-10-31 13:02:37Z fabian $ (Original squid RCS Id: a2m.c,v 1.1 1999/07/15 22:26:40 eddy Exp)
15 */
16
17 #include <stdio.h>
18 #include <stdlib.h>
19 #include <string.h>
20 #include "squid.h"
21 #include "msa.h"
22
23 /* Function: ReadA2M()
24 * Date: SRE, Sun Jun 6 17:11:29 1999 [bus from Madison 1999 worm mtg]
25 *
26 * Purpose: Parse an alignment read from an open A2M format
27 * alignment file. A2M is a single alignment format.
28 * Return the alignment, or NULL if we've already
29 * read the alignment.
30 *
31 * Args: afp - open alignment file
32 *
33 * Returns: MSA * - an alignment object.
34 * Caller responsible for an MSAFree()
35 */
36 MSA *
ReadA2M(MSAFILE * afp)37 ReadA2M(MSAFILE *afp)
38 {
39 MSA *msa;
40 char *buf;
41 char *name;
42 char *desc;
43 char *seq;
44 int idx;
45 int len1, len2;
46
47 if (feof(afp->f)) return NULL;
48
49 name = NULL;
50 msa = MSAAlloc(10, 0);
51 idx = 0;
52 while ((buf = MSAFileGetLine(afp)) != NULL)
53 {
54 if (*buf == '>')
55 {
56 buf++; /* skip the '>' */
57 if ((name = sre_strtok(&buf, WHITESPACE, &len1)) == NULL)
58 Die("Blank name in A2M file %s (line %d)\n", afp->fname, afp->linenumber);
59 desc = sre_strtok(&buf, "\n", &len2);
60
61 idx = GKIStoreKey(msa->index, name);
62 if (idx >= msa->nseqalloc) MSAExpand(msa);
63
64 msa->sqname[idx] = sre_strdup(name, len1);
65 if (desc != NULL) MSASetSeqDescription(msa, idx, desc);
66 msa->nseq++;
67 }
68 else if (name != NULL)
69 {
70 if ((seq = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) continue;
71 msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], seq, len1);
72 }
73 }
74 if (name == NULL) { MSAFree(msa); return NULL; }
75
76 MSAVerifyParse(msa);
77 return msa;
78 }
79
80
81 /* Function: WriteA2M()
82 * Date: SRE, Sun Jun 6 17:40:35 1999 [bus from Madison, 1999 worm mtg]
83 *
84 * Purpose: Write an "aligned FASTA" (aka a2m, to UCSC) formatted
85 * alignment.
86 *
87 * Args: fp - open FILE to write to.
88 * msa - alignment to write
89 *
90 * Returns: void
91 */
92 void
93 #ifdef CLUSTALO
94 /*WriteA2M(FILE *fp, MSA *msa, int vienna)*/
WriteA2M(FILE * fp,MSA * msa,int iWrap)95 WriteA2M(FILE *fp, MSA *msa, int iWrap)
96 #else
97 WriteA2M(FILE *fp, MSA *msa)
98 #endif
99 {
100 int idx; /* sequence index */
101 int pos; /* position in sequence */
102 #ifdef CLUSTALO
103 char *buf; /* buffer for writing seq */
104 int cpl = msa->alen<iWrap ? msa->alen+10 : (iWrap > 0 ? iWrap : 60); /* char per line (< 64) */
105 #else
106 char buf[64]; /* buffer for individual lines */
107 int cpl = 60; /* char per line; must be < 64 unless buf is bigger */
108 #endif
109
110 #ifdef CLUSTALO
111 if (NULL == (buf = (char *)malloc(cpl+20))){
112 Die("%s:%s:%d: could not malloc %d char for buffer",
113 __FUNCTION__, __FILE__, __LINE__, cpl+20);
114 }
115 else {
116 memset(buf, 0, cpl+20);
117 }
118 #endif
119
120
121 buf[cpl] = '\0';
122 for (idx = 0; idx < msa->nseq; idx++)
123 {
124 #ifdef CLUSTALO
125 /* most fasta sequences don't have a description, which
126 * leads to a trailing white space in the original code
127 */
128 fprintf(fp, ">%s", msa->sqname[idx]);
129
130 if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL /*&& !vienna*/) {
131 fprintf(fp, " %s", msa->sqdesc[idx]);
132 }
133 fprintf(fp, "\n");
134 #else
135 fprintf(fp, ">%s %s\n",
136 msa->sqname[idx],
137 (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) ? msa->sqdesc[idx] : "");
138 #endif
139 for (pos = 0; pos < msa->alen; pos+=cpl)
140 {
141 strncpy(buf, &(msa->aseq[idx][pos]), cpl);
142 /*if (vienna)
143 fprintf(fp, "%s", buf);
144 else*/
145 fprintf(fp, "%s\n", buf);
146 }
147 /*if (vienna)
148 fprintf(fp, "\n");*/
149
150 }
151
152 #ifdef CLUSTALO
153 free(buf); buf = NULL;
154 #endif
155
156 } /* this is the end of WriteA2M() */
157