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comparison 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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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 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) | |
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 * | |
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) | |
95 #else | |
96 WriteA2M(FILE *fp, MSA *msa) | |
97 #endif | |
98 { | |
99 int idx; /* sequence index */ | |
100 int pos; /* position in sequence */ | |
101 char buf[64]; /* buffer for individual lines */ | |
102 int cpl = 60; /* char per line; must be < 64 unless buf is bigger */ | |
103 | |
104 buf[cpl] = '\0'; | |
105 for (idx = 0; idx < msa->nseq; idx++) | |
106 { | |
107 #ifdef CLUSTALO | |
108 /* most fasta sequences don't have a description, which | |
109 * leads to a trailing white space in the original code | |
110 */ | |
111 fprintf(fp, ">%s", msa->sqname[idx]); | |
112 | |
113 if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL && !vienna) { | |
114 fprintf(fp, " %s", msa->sqdesc[idx]); | |
115 } | |
116 fprintf(fp, "\n"); | |
117 #else | |
118 fprintf(fp, ">%s %s\n", | |
119 msa->sqname[idx], | |
120 (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) ? msa->sqdesc[idx] : ""); | |
121 #endif | |
122 for (pos = 0; pos < msa->alen; pos+=cpl) | |
123 { | |
124 strncpy(buf, &(msa->aseq[idx][pos]), cpl); | |
125 if (vienna) | |
126 fprintf(fp, "%s", buf); | |
127 else | |
128 fprintf(fp, "%s\n", buf); | |
129 } | |
130 if (vienna) | |
131 fprintf(fp, "\n"); | |
132 | |
133 } | |
134 } |