diff source/fastq.c @ 0:816cb55b5a2d draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/source/fastq.c	Thu Jun 02 11:34:51 2016 -0400
@@ -0,0 +1,273 @@
+/****************************************************************************
+ * The 'FASTQ_ALL' structure group was used to store nucleotide sequence in
+ * fastq format, including basic operation function as well.
+ *
+ * This file was written by Haibin Xu, December 2011.
+ ****************************************************************************/
+
+#include "fastq.h"
+
+FASTQ_ALL *fastq_create()
+{
+	/* create a FASTQ_ALL sequence. If successful, return the point to it, 
+	 * otherwise, return NULL/.
+	 */
+	FASTQ_ALL *fq;
+	
+	if((fq=(FASTQ_ALL *)malloc(sizeof(FASTQ_ALL)))==NULL)
+		return NULL;
+
+	fq->description_1=NULL;
+	fq->sequence=NULL;
+	fq->description_2=NULL;
+	fq->quality=NULL;
+	
+	return fq;
+}
+
+int fastq_remove(FASTQ_ALL *fq)
+{
+	/* free the FASTQ sequence. If successful, return 0, otherwise return 1.
+	 */
+	if(fq==NULL)
+		return 1;
+	
+	if(fq->description_1!=NULL)
+		free(fq->description_1);
+	if(fq->sequence!=NULL)
+		free(fq->sequence);
+	if(fq->description_2!=NULL)
+		free(fq->description_2);
+	if(fq->quality!=NULL)
+		free(fq->quality);
+	
+	free(fq);
+	
+	return 0;
+}
+
+int fastq_clear(FASTQ_ALL *fq)
+{
+    /* clear the FASTQ sequence. If successful, return 0, otherwise return 1.
+     */
+    if(fq==NULL)
+        return 1;
+    
+	if(fq->description_1!=NULL)
+	{
+		free(fq->description_1);
+		fq->description_1=NULL;
+	}
+	if(fq->sequence!=NULL)
+	{
+		free(fq->sequence);
+		fq->sequence=NULL;
+	}
+	if(fq->description_2!=NULL)
+	{
+		free(fq->description_2);
+		fq->description_2=NULL;
+	}
+	if(fq->quality!=NULL)
+	{
+		free(fq->quality);
+		fq->quality=NULL;
+	}
+	
+    return 0;
+}
+
+long fastq_get_serial(FASTQ_ALL *fq)
+{
+    /* get sequence serial from FASTQ description in format '@serial_number'. 
+     * If successful return the serial, otherwise return -1.
+     */
+    long serial;
+    
+    if(fq==NULL || fq->description_1==NULL || fq->description_1[0]=='\0')
+        return -1;
+    
+    if((sscanf(fq->description_1, "@%ld", &serial))!=1)
+        return -1;
+    
+    return serial;
+}
+
+int fastq_scanf(FASTQ_ALL *fq, FILE *fp_in, 
+				int whether_append_description, int whether_append_quality)
+{
+	/* read a FASTQ sequence from input file, including description (whether_append_description=1)
+	 * or not (whether_append_description=0), including quality (whether_append_quality=1) or not
+	 * (whether_append_quality=0). If successful, return 0, otherwise, clear fq
+	 * and return 1.
+	 */
+	char description_1[FASTQ_DESCRIPTION_MAX_LENGTH], sequence[FASTQ_SEQUENCE_MAX_LENGTH];
+	char description_2[FASTQ_DESCRIPTION_MAX_LENGTH], quality[FASTQ_SEQUENCE_MAX_LENGTH];
+	
+	char *p_description_1, *p_sequence, *p_description_2, *p_quality;
+	
+    if(fp_in==NULL || fq==NULL)
+        return 1;
+    
+	fastq_clear(fq);
+
+	/* read the FASTQ sequence */
+    fgets(description_1, FASTQ_DESCRIPTION_MAX_LENGTH, fp_in);
+    fgets(sequence, FASTQ_SEQUENCE_MAX_LENGTH, fp_in);
+    fgets(description_2, FASTQ_DESCRIPTION_MAX_LENGTH, fp_in);
+    fgets(quality, FASTQ_SEQUENCE_MAX_LENGTH, fp_in);
+	
+	/* check whether integrity of the FASTQ sequence */
+    if(description_1[0]=='\0' || sequence[0]=='\0' || description_2[0]=='\0' ||
+	   quality[0]=='\0' || description_1[0]!='@'|| description_2[0]!='+' ||
+	   description_1[strlen(description_1)-1]!='\n' ||
+	   sequence[strlen(sequence)-1]!='\n' ||
+	   description_2[strlen(description_2)-1]!='\n')
+        return 1;
+
+	/* remove return character at the end */
+	if(description_1[strlen(description_1)-1]=='\n')
+		description_1[strlen(description_1)-1]='\0';
+	if(sequence[strlen(sequence)-1]=='\n')
+		sequence[strlen(sequence)-1]='\0';
+	if(description_2[strlen(description_2)-1]=='\n')
+		description_2[strlen(description_2)-1]='\0';
+	if(quality[strlen(quality)-1]=='\n')
+		quality[strlen(quality)-1]='\0';
+	
+	/* append the sequence information to fq */
+	if((p_sequence=(char *)malloc(strlen(sequence)+1))==NULL)
+		return 1;
+	strcpy(p_sequence, sequence);
+	fq->sequence=p_sequence;
+	
+	if(whether_append_quality==1)
+	{
+		if((p_quality=(char *)malloc(strlen(quality)+1))==NULL)
+		{
+			fastq_clear(fq);
+			return 1;
+		}
+		strcpy(p_quality, quality);
+		fq->quality=p_quality;
+	}
+	if(whether_append_description==1)
+	{
+		if((p_description_1=(char *)malloc(strlen(description_1)+1))==NULL)
+		{
+			fastq_clear(fq);
+			return 1;
+		}
+		strcpy(p_description_1, description_1);
+		fq->description_1=p_description_1;
+		
+		if((p_description_2=(char *)malloc(strlen(description_2)+1))==NULL)
+		{
+			fastq_clear(fq);
+			return 1;
+		}
+		strcpy(p_description_2, description_2);
+		fq->description_2=p_description_2;
+	}
+
+    return 0;
+}
+
+int fastq_printf(FASTQ_ALL *fq, FILE *fp_out, char *format, long serial)
+{
+    /* write sequence into output file in FASTQ format(format='fq') or FASTA format(format='fa')
+	 * using the original description (serial=-1) or the new serial.
+	 * If successful, return 0, otherwise return 1.
+     */
+    if(fp_out==NULL || fq==NULL)
+        return 1;
+    
+	if(strcmp(format, "fq")==0) /* output in FASTQ format */
+	{
+		if(serial==-1)
+		{
+			if(fq->description_1!=NULL)
+			{
+				fputs(fq->description_1, fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->sequence, fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->description_2, fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->quality, fp_out);
+				fputc('\n', fp_out);
+			}
+			else
+			{
+				fputc('@', fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->sequence, fp_out);
+				fputc('\n', fp_out);
+				fputc('+', fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->quality, fp_out);
+				fputc('\n', fp_out);				
+			}
+		}
+		else
+		{
+			fprintf(fp_out, "@%ld\n",  serial);
+			fputs(fq->sequence, fp_out);
+			fputc('\n', fp_out);
+			fprintf(fp_out, "+%ld\n",  serial);
+			fputs(fq->quality, fp_out);
+			fputc('\n', fp_out);
+		}
+	}
+	else if(strcmp(format, "fa")==0) /* output in FASTQ format */
+	{
+		if(serial==-1)
+		{
+			if(fq->description_1!=NULL)
+			{
+				fputc('>', fp_out);
+				fputs(&(fq->description_1[1]), fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->sequence, fp_out);
+				fputc('\n', fp_out);
+			}
+			else
+			{
+				fputc('>', fp_out);
+				fputc('\n', fp_out);
+				fputs(fq->sequence, fp_out);
+				fputc('\n', fp_out);
+			}
+		}
+		else
+		{
+			fprintf(fp_out, ">%ld\n",  serial);
+			fputs(fq->sequence, fp_out);
+			fputc('\n', fp_out);
+		}
+	}
+	else
+		return 1;
+	
+    return 0;
+}
+
+long fastq_get_length(FASTQ_ALL *fq)
+{
+	/* return the length of FASTQ sequence, is any error, return -1
+	 */
+	
+	if(fq==NULL)
+		return -1;
+	if(fq->sequence==NULL)
+		return 0;
+	return strlen(fq->sequence);
+}
+
+
+
+
+
+
+
+