functions for processing dna

src/zmapUtils/zmapDNAUtils.c

+/*  File: zmapDNAUtils.c
+ *  Author: Ed Griffiths (edgrif@sanger.ac.uk)
+ *  Copyright (c) Sanger Institute, 2005
+ *-------------------------------------------------------------------
+ * ZMap is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
+ *-------------------------------------------------------------------
+ * This file is part of the ZMap genome database package
+ * originated by
+ * 	Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ *      Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
+ *
+ * Description: General functions for doing stuff with DNA strings.
+ *
+ * Exported functions: See XXXXXXXXXXXXX.h
+ * HISTORY:
+ * Last edited: Nov  8 16:33 2005 (edgrif)
+ * Created: Tue Nov  8 13:47:27 2005 (edgrif)
+ * CVS info:   $Id: zmapDNAUtils.c,v 1.1 2005-11-08 17:06:15 edgrif Exp $
+ *-------------------------------------------------------------------
+ */
+
+#include <string.h>
+#include <ZMap/zmapUtils.h>
+#include <ZMap/zmapUtilsDNA.h>
+
+
+
+/* FASTA files can lines of any length but 50 is convenient for terminal display
+ * and counting... */
+enum {FASTA_CHARS = 50} ;
+
+
+/* This code is lifted from the code that I wrote for acedb - EG
+ * Given a sequence name and its dna sequence, will dump the data in FastA
+ * format.
+ * Routine could be extended to find the sequence length but tedious/trivial really. */
+gboolean zmapDNADumpFASTA(GIOChannel *file, char *seq_name, int seq_len, char *dna, GError **error_out)
+{
+  gboolean result = TRUE ;
+  GIOStatus status ;
+  gsize bytes_written = 0 ;
+  char *header ;
+  char buffer[FASTA_CHARS + 2] ;			    /* FastA chars + \n + \0 */
+  int dna_length  = 0 ;
+  int lines = 0, chars_left = 0 ;
+  char *cp = NULL ;
+  int i ;
+
+  zMapAssert(file && seq_name && seq_len > 0 && dna && error_out) ;
+
+  header = g_strdup_printf(">%s\n", seq_name) ;
+
+  if ((status = g_io_channel_write_chars(file, header, -1, &bytes_written, error_out))
+      != G_IO_STATUS_NORMAL)
+    {
+      result = FALSE ;
+    }
+  else
+    {
+      dna_length = strlen(dna) ;
+      lines = dna_length / FASTA_CHARS ;
+      chars_left = dna_length % FASTA_CHARS ;
+      cp = dna ;
+
+      /* Do the full length lines.                                           */
+      if (lines != 0)
+	{
+	  buffer[FASTA_CHARS] = '\n' ;
+	  buffer[FASTA_CHARS + 1] = '\0' ; 
+	  for (i = 0 ; i < lines && result ; i++)
+	    {
+	      memcpy(&buffer[0], cp, FASTA_CHARS) ;
+	      cp += FASTA_CHARS ;
+
+	      if ((status = g_io_channel_write_chars(file, &buffer[0], -1, &bytes_written, error_out))
+		  != G_IO_STATUS_NORMAL)
+		result = FALSE ;
+	    }
+	}
+
+      /* Do the last line.                                                   */
+      if (chars_left != 0)
+	{
+	  memcpy(&buffer[0], cp, chars_left) ;
+	  buffer[chars_left] = '\n' ;
+	  buffer[chars_left + 1] = '\0' ; 
+	  if ((status = g_io_channel_write_chars(file, &buffer[0], -1, &bytes_written, error_out))
+	      != G_IO_STATUS_NORMAL)
+	    result = FALSE ;
+	}
+    }
+
+  g_free(header) ;
+
+  return result ;
+}
+
+