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Successfully reading and writing fasta files.
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@iamthad
iamthad committed Nov 21, 2012
1 parent ae73058 commit cadf427
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Showing 4 changed files with 123 additions and 62 deletions.
48 changes: 16 additions & 32 deletions CProject/doubly_linked_list.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2,38 +2,6 @@
#include <stdlib.h>
#include "doubly_linked_list.h"

/*int main(){
dll a;
dln * x, * y, * z, * t;
a.first = NULL;
a.last = NULL;
x = malloc(sizeof(dln));
insertBeginning(&a,x);
x -> val = 1;
printf("x at: %p,val = %d, next = %p, prev = %p\n",x,x->val,x->next,x->prev);
y = malloc(sizeof(dln));
insertEnd(&a,y);
y -> val = 3;
z = malloc(sizeof(dln));
printf("y at: %p,val = %d, next = %p, prev = %p\n",y,y->val,y->next,y->prev);
insertBefore(&a,y,z);
t = a.first;
printf("z at: %p,val = %d, next = %p, prev = %p\n",z,z->val,z->next,z->prev);
do{
printf("At %p: %d\n",t,t->val);
printf("Changing to %p\n",t->next);
t = t->next;
}while (t -> next != NULL);
return 0;
}*/
void insertAfter(dll * list, dln * node, dln * new){
new -> prev = node;
new -> next = node -> next;
Expand Down Expand Up @@ -83,3 +51,19 @@ void dllremove(dll * list, dln * node){
node -> next -> prev = node -> prev;
free(node);
}

void dllclear(dll * list){
dln * node, * next;
node = list -> first;
while(node != NULL){
next = node -> next;
dllremove(list,node);
node = next;
}
}

void dllfree(dll * list){
dllclear(list);
free(list);
}

2 changes: 2 additions & 0 deletions CProject/doubly_linked_list.h
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Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,5 @@ void insertBefore(dll * list, dln * node, dln * new);
void insertBeginning(dll * list, dln * new);
void insertEnd(dll * list, dln * node);
void dllremove(dll * list, dln * node);
void dllclear(dll * list);
void dllfree(dll * list);
126 changes: 96 additions & 30 deletions CProject/fasta.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3,62 +3,62 @@
#include "doubly_linked_list.h"
#include "fasta.h"

#define SCANNING_HEADER 1
#define SCANNING_SEQUENCE 2
#define READING_HEADER 3
#define READING_SEQUENCE 4
#define HEADER_LENGTH 80

int fasta_read(char * filename, dll * sequences){

FILE *file;
FILE *file, *debugfile;
int num_sequences = 0;
int c=0;
int mode = 0;
int location = 0;
int sequence_length = 0;
int sequence_index = 0;
int header_index = 0;
dln * sequence = NULL;

file = fopen(*filename, "r");
file = fopen(filename, "r");
if(file == NULL){
perror("Error with input file");
exit(1);
}
debugfile = fopen("/dev/null/","w");
do{
c = fgetc(file);
switch (c){
case '\n':
if (mode == SCANNING_HEADER){
mode = SCANNING_SEQUENCE;
printf("Scanning sequence.\n");
fprintf(debugfile,"Scanning sequence.\n");
}

if (mode == READING_HEADER){
mode = READING_SEQUENCE;
sequence_index = 0;
printf("Reading sequence.\n");
fprintf(debugfile,"Reading sequence.\n");
}
break;

case '>':
switch (mode){
case SCANNING_SEQUENCE:
fseek(file,location,SEEK_SET);
if (temp != NULL)
insertEnd(&sequences,temp);
initialize_sequence(temp, sequence_length);
if (sequence != NULL){
fprintf(debugfile,"Putting sequence into list at location %p\n",sequences);
insertEnd(sequences,sequence);
}
fprintf(debugfile,"Initialize sequence.\n");
sequence = initialize_sequence(sequence_length);
fprintf(debugfile,"%p\n",sequence);
sequence_length = 0;
mode = READING_HEADER;
header_index = 0;
printf("Reading header.\n");
fprintf(debugfile,"Reading header.\n");
break;
case READING_SEQUENCE:
default:
mode = SCANNING_HEADER;
printf("Scanning header.\n");
fprintf(debugfile,"Scanning header.\n");
location = ftell(file);
printf("Location: %d\n",location);
fprintf(debugfile,"Location: %d\n",location);
break;
}
num_sequences++;
Expand All @@ -68,16 +68,17 @@ int fasta_read(char * filename, dll * sequences){
switch (mode){
case SCANNING_SEQUENCE:
fseek(file,location,SEEK_SET);
if (temp != NULL)
insertEnd(&sequences,temp);
initialize_sequence(temp, sequence_length);
if (sequence != NULL)
insertEnd(sequences,sequence);
sequence = initialize_sequence(sequence_length);
fprintf(debugfile,"%p\n",sequence);
sequence_length = 0;
mode = READING_HEADER;
header_index = 0;
printf("Reading header.\n");
fprintf(debugfile,"Reading header.\n");
break;
case READING_SEQUENCE:
insertEnd(&sequences,temp);
insertEnd(sequences,sequence);
break;
default:
fprintf(stderr,"Hit end of file unexpectedly.\n");
Expand All @@ -98,20 +99,30 @@ int fasta_read(char * filename, dll * sequences){
fprintf(stderr,"Header would have overflowed.\n");
exit(1);
}
temp -> header[header_index] = c;
header_index++;
if(sequence != NULL){
sequence -> header[header_index] = c;
header_index++;
}else{
fprintf(stderr,"Sequence does not exist.\n");
exit(1);
}
break;
case READING_SEQUENCE:
if (sequence_index > temp -> sequence_length){
if (sequence_index > sequence -> sequence_length){
fprintf(stderr,"Sequence would have overflowed.\n");
exit(1);
}
temp -> data[sequence_index] = c;
sequence_index++;
if(sequence != NULL){
sequence -> data[sequence_index] = c;
sequence_index++;
}else{
fprintf(stderr,"Sequence does not exist.\n");
exit(1);
}
break;
}
}
}while(c!=EOF);
}while(!feof(file));



Expand All @@ -121,8 +132,63 @@ int fasta_read(char * filename, dll * sequences){

}

int initialize_sequence(dln * sequence, int sequence_length){
sequence = malloc(sizeof(dln)+(sequence_length+1)*sizeof(char));
int fasta_write(char * filename, dll * sequences){
FILE *file;
dln * sequence;
file = fopen(filename,"w");
int i, column = 0, c;
int column_length = 60;
if(file == NULL){
perror("Error with output file");
exit(1);
}
if(sequences == NULL){
fprintf(stderr,"Sequences is undefined for writing.\n");
exit(1);
}
sequence = sequences -> first;
while(sequence != NULL){
// Print header
fprintf(file,">");
for(i=0;i<=HEADER_LENGTH; i++){
c = sequence->header[i];
if(c != 0)
fprintf(file,"%c",c);
else{
break;
}
}
fprintf(file,"\n");

// Print sequence
for(i=0;i<=sequence->sequence_length;i++){
c = sequence->data[i];
if(c != 0){
fprintf(file,"%c",c);
column++;
}
else{
fprintf(file,"\n");
column = 0;
break;
}
if(column==column_length){
fprintf(file,"\n");
column = 0;
}
}
fprintf(file,"\n");
sequence = sequence->next;
}
return 0;

}

dln * initialize_sequence(int sequence_length){
int i, length;
dln * sequence;
length = sizeof(dln)+(sequence_length+1)*sizeof(char);
sequence = malloc(length);
if(sequence != NULL){
sequence -> sequence_length = sequence_length;
for(i = 0; i<=sequence_length; i++){
Expand All @@ -131,7 +197,7 @@ int initialize_sequence(dln * sequence, int sequence_length){
for(i = 0; i<=HEADER_LENGTH; i++){
sequence -> header[i] = 0;
}
return 0;
return sequence;
}else{
fprintf(stderr,"Error allocating memory.\n");
exit(1);
Expand Down
9 changes: 9 additions & 0 deletions CProject/fasta.h
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Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
#define SCANNING_HEADER 1
#define SCANNING_SEQUENCE 2
#define READING_HEADER 3
#define READING_SEQUENCE 4
#define HEADER_LENGTH 80

int fasta_read(char * filename, dll * sequences);
int fasta_write(char * filename, dll * sequences);
dln * initialize_sequence(int sequence_length);

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