+++ /dev/null
-/*****************************************************************
- * 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.
- *****************************************************************/
-
-/* phylip.c
- * SRE, Mon Jun 14 14:08:33 1999 [St. Louis]
- *
- * Import/export of PHYLIP interleaved multiple sequence alignment
- * format files.
- *
- * 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)
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include "squid.h"
-#include "msa.h"
-
-#ifdef TESTDRIVE_PHYLIP
-/*****************************************************************
- * phylip.c test driver:
- *
- */
-int
-main(int argc, char **argv)
-{
- MSAFILE *afp;
- MSA *msa;
- char *file;
-
- file = argv[1];
-
- if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL)
- Die("Couldn't open %s\n", file);
-
- printf("format %d\n", afp->format);
-
- while ((msa = ReadPhylip(afp)) != NULL)
- {
- WritePhylip(stdout, msa);
- MSAFree(msa);
- }
-
- MSAFileClose(afp);
- exit(0);
-}
-/******************************************************************/
-#endif /* testdrive_phylip */
-
-
-
-/* Function: ReadPhylip()
- * Date: SRE, Fri Jun 18 12:59:37 1999 [Sanger Centre]
- *
- * Purpose: Parse an alignment from an open Phylip format
- * alignment file. Phylip is a single-alignment format.
- * Return the alignment, or NULL if we have no data.
- *
- * Args: afp - open alignment file
- *
- * Returns: MSA * - an alignment object
- * Caller responsible for an MSAFree()
- * NULL if no more alignments
- */
-MSA *
-ReadPhylip(MSAFILE *afp)
-{
- MSA *msa;
- char *s, *s1, *s2;
- char name[11]; /* seq name max len = 10 char */
- int nseq, alen;
- int idx; /* index of current sequence */
- int slen;
- int nblock;
-
- if (feof(afp->f)) return NULL;
-
- /* Skip until we see a nonblank line; it's the header,
- * containing nseq/alen
- */
- nseq = 0; alen = 0;
- while ((s = MSAFileGetLine(afp)) != NULL)
- {
- if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue;
- if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL)
- Die("Failed to parse nseq/alen from first line of PHYLIP file %s\n", afp->fname);
- if (! IsInt(s1) || ! IsInt(s2))
- Die("nseq and/or alen not an integer in first line of PHYLIP file %s\n", afp->fname);
- nseq = atoi(s1);
- alen = atoi(s2);
- break;
- }
-
- msa = MSAAlloc(nseq, 0);
- idx = 0;
- nblock = 0;
- while ((s = MSAFileGetLine(afp)) != NULL)
- {
- /* ignore blank lines. nonblank lines start w/ nonblank char */
- if (isspace(*s)) continue;
- /* First block has seq names */
- if (nblock == 0) {
- strncpy(name, s, 10);
- name[10] = '\0';
- GKIStoreKey(msa->index, name);
- msa->sqname[idx] = sre_strdup(name, -1);
- s += 10;
- }
- /* be careful of trailing whitespace on lines */
- if ((s1 = sre_strtok(&s, WHITESPACE, &slen)) == NULL)
- Die("Failed to parse sequence at line %d of PHYLIP file %s\n",
- afp->linenumber, afp->fname);
- msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], s1, slen);
-
- idx++;
- if (idx == nseq) { idx = 0; nblock++; }
- }
- msa->nseq = nseq;
- MSAVerifyParse(msa); /* verifies; sets alen, wgt; frees sqlen[] */
- return msa;
-}
-
-
-
-/* Function: WritePhylip()
- * Date: SRE, Fri Jun 18 12:07:41 1999 [Sanger Centre]
- *
- * Purpose: Write an alignment in Phylip format to an open file.
- *
- * Args: fp - file that's open for writing.
- * msa - alignment to write.
- *
- * Returns: (void)
- */
-void
-WritePhylip(FILE *fp, MSA *msa)
-{
- int idx; /* counter for sequences */
- int cpl = 50; /* 50 seq char per line */
- char buf[51]; /* buffer for writing seq */
- int pos;
-
- /* First line has nseq, alen
- */
- fprintf(fp, " %d %d\n", msa->nseq, msa->alen);
-
- /* Alignment section.
- * PHYLIP is a multiblock format, blocks (optionally) separated
- * by blanks; names only attached to first block. Names are
- * restricted to ten char; we achieve this by simple truncation (!).
- * (Do we need to convert gap characters from our ./- convention?)
- */
- for (pos = 0; pos < msa->alen; pos += cpl)
- {
- if (pos > 0) fprintf(fp, "\n");
-
- for (idx = 0; idx < msa->nseq; idx++)
- {
- strncpy(buf, msa->aseq[idx] + pos, cpl);
- buf[cpl] = '\0';
- if (pos > 0) fprintf(fp, "%s\n", buf);
- else fprintf(fp, "%-10.10s%s\n", msa->sqname[idx], buf);
- }
- }
- return;
-}
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