Mercurial > repos > clustalomega > clustalomega
comparison clustalomega/clustal-omega-1.0.2/src/squid/phylip.c @ 1:bc707542e5de
Uploaded
author | clustalomega |
---|---|
date | Thu, 21 Jul 2011 13:35:08 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
0:ff1768533a07 | 1:bc707542e5de |
---|---|
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 /* phylip.c | |
11 * SRE, Mon Jun 14 14:08:33 1999 [St. Louis] | |
12 * | |
13 * Import/export of PHYLIP interleaved multiple sequence alignment | |
14 * format files. | |
15 * | |
16 * RCS $Id: phylip.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: phylip.c,v 1.1 1999/07/15 22:29:20 eddy Exp) | |
17 */ | |
18 | |
19 #include <stdio.h> | |
20 #include <stdlib.h> | |
21 #include <string.h> | |
22 #include <ctype.h> | |
23 #include "squid.h" | |
24 #include "msa.h" | |
25 | |
26 #ifdef TESTDRIVE_PHYLIP | |
27 /***************************************************************** | |
28 * phylip.c test driver: | |
29 * | |
30 */ | |
31 int | |
32 main(int argc, char **argv) | |
33 { | |
34 MSAFILE *afp; | |
35 MSA *msa; | |
36 char *file; | |
37 | |
38 file = argv[1]; | |
39 | |
40 if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL) | |
41 Die("Couldn't open %s\n", file); | |
42 | |
43 printf("format %d\n", afp->format); | |
44 | |
45 while ((msa = ReadPhylip(afp)) != NULL) | |
46 { | |
47 WritePhylip(stdout, msa); | |
48 MSAFree(msa); | |
49 } | |
50 | |
51 MSAFileClose(afp); | |
52 exit(0); | |
53 } | |
54 /******************************************************************/ | |
55 #endif /* testdrive_phylip */ | |
56 | |
57 | |
58 | |
59 /* Function: ReadPhylip() | |
60 * Date: SRE, Fri Jun 18 12:59:37 1999 [Sanger Centre] | |
61 * | |
62 * Purpose: Parse an alignment from an open Phylip format | |
63 * alignment file. Phylip is a single-alignment format. | |
64 * Return the alignment, or NULL if we have no data. | |
65 * | |
66 * Args: afp - open alignment file | |
67 * | |
68 * Returns: MSA * - an alignment object | |
69 * Caller responsible for an MSAFree() | |
70 * NULL if no more alignments | |
71 */ | |
72 MSA * | |
73 ReadPhylip(MSAFILE *afp) | |
74 { | |
75 MSA *msa; | |
76 char *s, *s1, *s2; | |
77 char name[11]; /* seq name max len = 10 char */ | |
78 int nseq, alen; | |
79 int idx; /* index of current sequence */ | |
80 int slen; | |
81 int nblock; | |
82 | |
83 if (feof(afp->f)) return NULL; | |
84 | |
85 /* Skip until we see a nonblank line; it's the header, | |
86 * containing nseq/alen | |
87 */ | |
88 nseq = 0; alen = 0; | |
89 while ((s = MSAFileGetLine(afp)) != NULL) | |
90 { | |
91 if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; | |
92 if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) | |
93 Die("Failed to parse nseq/alen from first line of PHYLIP file %s\n", afp->fname); | |
94 if (! IsInt(s1) || ! IsInt(s2)) | |
95 Die("nseq and/or alen not an integer in first line of PHYLIP file %s\n", afp->fname); | |
96 nseq = atoi(s1); | |
97 alen = atoi(s2); | |
98 break; | |
99 } | |
100 | |
101 msa = MSAAlloc(nseq, 0); | |
102 idx = 0; | |
103 nblock = 0; | |
104 while ((s = MSAFileGetLine(afp)) != NULL) | |
105 { | |
106 /* ignore blank lines. nonblank lines start w/ nonblank char */ | |
107 if (isspace(*s)) continue; | |
108 /* First block has seq names */ | |
109 if (nblock == 0) { | |
110 strncpy(name, s, 10); | |
111 name[10] = '\0'; | |
112 GKIStoreKey(msa->index, name); | |
113 msa->sqname[idx] = sre_strdup(name, -1); | |
114 s += 10; | |
115 } | |
116 /* be careful of trailing whitespace on lines */ | |
117 if ((s1 = sre_strtok(&s, WHITESPACE, &slen)) == NULL) | |
118 Die("Failed to parse sequence at line %d of PHYLIP file %s\n", | |
119 afp->linenumber, afp->fname); | |
120 msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], s1, slen); | |
121 | |
122 idx++; | |
123 if (idx == nseq) { idx = 0; nblock++; } | |
124 } | |
125 msa->nseq = nseq; | |
126 MSAVerifyParse(msa); /* verifies; sets alen, wgt; frees sqlen[] */ | |
127 return msa; | |
128 } | |
129 | |
130 | |
131 | |
132 /* Function: WritePhylip() | |
133 * Date: SRE, Fri Jun 18 12:07:41 1999 [Sanger Centre] | |
134 * | |
135 * Purpose: Write an alignment in Phylip format to an open file. | |
136 * | |
137 * Args: fp - file that's open for writing. | |
138 * msa - alignment to write. | |
139 * | |
140 * Returns: (void) | |
141 */ | |
142 void | |
143 WritePhylip(FILE *fp, MSA *msa) | |
144 { | |
145 int idx; /* counter for sequences */ | |
146 int cpl = 50; /* 50 seq char per line */ | |
147 char buf[51]; /* buffer for writing seq */ | |
148 int pos; | |
149 | |
150 /* First line has nseq, alen | |
151 */ | |
152 fprintf(fp, " %d %d\n", msa->nseq, msa->alen); | |
153 | |
154 /* Alignment section. | |
155 * PHYLIP is a multiblock format, blocks (optionally) separated | |
156 * by blanks; names only attached to first block. Names are | |
157 * restricted to ten char; we achieve this by simple truncation (!). | |
158 * (Do we need to convert gap characters from our ./- convention?) | |
159 */ | |
160 for (pos = 0; pos < msa->alen; pos += cpl) | |
161 { | |
162 if (pos > 0) fprintf(fp, "\n"); | |
163 | |
164 for (idx = 0; idx < msa->nseq; idx++) | |
165 { | |
166 strncpy(buf, msa->aseq[idx] + pos, cpl); | |
167 buf[cpl] = '\0'; | |
168 if (pos > 0) fprintf(fp, "%s\n", buf); | |
169 else fprintf(fp, "%-10.10s%s\n", msa->sqname[idx], buf); | |
170 } | |
171 } | |
172 return; | |
173 } |