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buttercup.c
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buttercup.c
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/*Buttercup - objective from a fixrank file, pull out original
fastq sequence information*/
#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <getopt.h>
#include <string.h>
#include "search.h"
#include <errno.h>
/*argument collection and start of agorithm*/
struct files {
FILE *outfile;
FILE *fixrank;
FILE *fastq;
};
struct split_data {
char **tokenize;
int elements;
};
struct data {
char *taxlevel;
char *name;
};
void errorOut(struct files *f, struct data *d) {
printf("It seems the required files are not inputted, please, try again\n");
exit(-10);
}
/*last element is a single '\0' character*/
struct split_data *splitData(char *tokenize, const char *delim) {
char **data;
char *tmpToken = NULL, *tmpStringLoc, *tmp = strdup(tokenize);
int elements = 0;
struct split_data *info = (struct split_data*) malloc(sizeof(struct split_data));
/*tmp is used to leave the original char * the same*/
tmpToken = strtok_r(tmp, delim, &tmpStringLoc);
while (tmpToken != NULL) {
elements++;
if (elements == 1) {
(info->tokenize) = (char **)malloc(elements *sizeof(char *));
} else {
(info->tokenize) = (char **)realloc(info->tokenize, (elements+1) * sizeof(char *));
}
(info->tokenize)[elements-1] = strdup(tmpToken);
tmpToken = strtok_r(NULL, delim, &tmpStringLoc);
}
(info->tokenize)[elements] = strdup("\0");
info->elements = elements;
return info;
}
char *PadWithZeros(char *s) {
const char *padding = "0000000";
char *news;
news = (char *)malloc(sizeof(char) * 7);
int len = 5 - strlen(s);
sprintf(news, "%*.*s%s\0", len, len, padding, s);
return news;
}
void DiveThroughFixrank(struct tree *t, FILE *fixrank, char *taxlevel, char *name) {
char *line = NULL;
size_t length;
ssize_t read;
char *s;
char *tmp;
long long int id;
struct split_data *nameSearch = (struct split_data*)malloc(sizeof(struct split_data));
struct split_data *idFirst = (struct split_data*)malloc(sizeof(struct split_data));
struct split_data *idLast = (struct split_data*)malloc(sizeof(struct split_data));
int i = 0;
/*Read the entire file*/
while ((read = getline(&line, &length, fixrank)) != -1) {
nameSearch = splitData(line, "\t");
for (i = 0; i < nameSearch->elements; i++) {
/*if there is a match, the next should be taxlevel*/
if (strcmp(name, (nameSearch->tokenize)[i]) == 0) {
if (strcmp(taxlevel, (nameSearch->tokenize)[i+1]) == 0) {
idLast = splitData((nameSearch->tokenize)[0], "|");
idFirst = splitData((idLast->tokenize)[0], ":");
s = (char *)malloc(100*sizeof(char));
(idFirst->tokenize)[5] = PadWithZeros((idFirst->tokenize)[5]);
(idFirst->tokenize)[6] = PadWithZeros((idFirst->tokenize)[6]);
sprintf(s, "%s%s%s%s", (idFirst->tokenize)[1], (idFirst->tokenize)[4], (idFirst->tokenize)[5], (idFirst->tokenize)[6]);
id = strtoll(s, &tmp, 0);
free(s);
AddNode(&(t->root), id);
(t->count)++;
}
free((nameSearch->tokenize)[i]);
}
}
}
//printf("%d\n", (t->count));
}
void PullOutMatchedReads(struct tree *t, FILE *fastq, FILE *out) {
int location = 0;
int write = 0;
char *line = NULL;
size_t length;
ssize_t read;
struct split_data *idFirst;
struct split_data *idLast;
char *tmp;
char *s;
long long int id = 0;
int i = 0;
while ((read = getline(&line, &length, fastq)) != -1) {
if (location == 0) {
idFirst = (struct split_data*)malloc(sizeof(struct split_data));
idLast = (struct split_data*)malloc(sizeof(struct split_data));
idFirst = splitData(line, " ");
idLast = splitData((idFirst->tokenize)[0], ":");
s = (char *)malloc(100*sizeof(char));
(idLast->tokenize)[idLast->elements-2] = PadWithZeros((idLast->tokenize)[idLast->elements-2]);
(idLast->tokenize)[idLast->elements-1] = PadWithZeros((idLast->tokenize)[idLast->elements-1]);
sprintf(s, "%s%s%s%s", (idLast->tokenize)[1], (idLast->tokenize)[idLast->elements-3], (idLast->tokenize)[idLast->elements-2], (idLast->tokenize)[idLast->elements-1]);
id = strtoll(s, &tmp, 0);
write = Lookup(t->root, id);
location++;
for (i = 0; i < idFirst->elements; i++) {
free((idFirst->tokenize)[i]);
}
free((idFirst->tokenize));
free(idFirst);
for (i = 0; i < idLast->elements; i++) {
free((idLast->tokenize)[i]);
}
free((idLast->tokenize));
free(idLast);
free(s);
} else if (location == 3) {
location = 0;
} else {
location++;
}
if (write) {
fprintf(out, "%s", line);
}
}
}
void CreateSearchTree(struct files *f, struct data *d) {
struct tree *t = (struct tree *)malloc(sizeof(struct tree));
t->root = NULL;
DiveThroughFixrank(t, f->fixrank, d->taxlevel, d->name);
PullOutMatchedReads(t, f->fastq, f->outfile);
}
int main(int argc, char *argv[]) {
int cmd_line_char, long_index;
struct files requiredFiles;
struct data taxInfo;
const struct option longopts[] = {
{"version", no_argument, 0, 'v'},
{"help", no_argument, 0, 'h'},
{"outfile", required_argument, 0, 'o'},
{"fastq", required_argument, 0, 'f'},
{"fixrank", required_argument, 0, 'r'},
{"tax_level", required_argument, 0, 'l'},
{"name", required_argument, 0, 'n',},
{0, 0, 0, 0}
};
while ((cmd_line_char = getopt_long(argc, argv, "vho:f:r:l:n:", longopts, &long_index)) != EOF) {
switch(cmd_line_char) {
case 'h':
printf("To use butter cup, please supply -o outputfile -f fastq file -r fixrank file and -l taxLevel -n tax Name\n");
printf("./Buttercup -o buttercup.out.fq -f <(zcat /mnt/home/alida/scratch/pplacer/vag_cancer/cancer.extendedFrags.fastq.gz) -r /mnt/home/alida/scratch/pplacer/vag_cancer/classify.fixrank -l genus -n Lactobacillus\n\n");
exit(0);
case 'o':
requiredFiles.outfile = fopen(optarg, "w");
if (requiredFiles.outfile == NULL) {
errorOut(&requiredFiles, &taxInfo);
}
break;
case 'f':
requiredFiles.fastq = fopen(optarg, "r");
if (requiredFiles.fastq == NULL) {
errorOut(&requiredFiles, &taxInfo);
}
break;
case 'r':
requiredFiles.fixrank = fopen(optarg, "r");
if (requiredFiles.fixrank == NULL) {
errorOut(&requiredFiles, &taxInfo);
}
break;
case 'l':
taxInfo.taxlevel = strdup(optarg);
break;
case 'n':
taxInfo.name = strdup(optarg);
break;
}
}
CreateSearchTree(&requiredFiles, &taxInfo);
return 0;
}