1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
/**
* FileName: sequence.h
* Authors: Tiayyba Riaz, Celine Mercier
* Description: Prototypes and other declarations for sequences
* **/
#ifndef SEQUENCE_H_
#define SEQUENCE_H_
#include <stdint.h>
#include <stdio.h>
#include "../libutils/utilities.h"
#include "fasta_header_parser.h"
typedef struct {
char* accession_id; // identifier
char *rawheader; // not parsed header
element_from_header* header; // parsed header
char *sequence; // DNA sequence itself
int32_t length; // DNA sequence's length
int32_t count; // abundance of the sequence
unsigned char *table; // 4mer occurrence table build using function buildTable
int32_t over; // count of 4mer with occurrences greater than 255 (overflow)
struct fastaSeqPtr* next; // next unique sequence for example
BOOL cluster_center; // whether the sequence is a cluster center or not
int32_t cluster_weight; // cluster weight when sequence is cluster center
int32_t cluster_weight_unique_ids; // cluster weight when sequence is cluster center, counting the number sequence records
double score; // score with cluster center for example
struct fastaSeqPtr* center; // pointer to the sequence's cluster center
int32_t center_index; // index of the sequence's cluster center
BOOL uniqHead; // whether the sequence is a unique head or not
char* columns_BIOM; // to print in BIOM format
int columns_BIOM_size; // size allocated for columns_BIOM
char* line_OTU_table; // to print in OTU table format
int line_OTU_table_size; // size allocated for line_OTU_table
struct hashtable *sample_counts; // sample counts for sumaclean
}fastaSeq,*fastaSeqPtr;
typedef struct {
int32_t count;
fastaSeqPtr fastaSeqs;
}fastaSeqCount, *fastaSeqCountPtr;
fastaSeqPtr seq_getNext(FILE *fp, char *fieldDelim, BOOL isStandardSeq, BOOL onlyATGC);
char *seq_readNextFromFilebyLine(FILE* fp);
void seq_fillSeq(char *seq, fastaSeqPtr seqElem, int seqLen);
void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen);
void seq_fillDigitSeq(char *seq, fastaSeqPtr seqElem, int seqLen);
void seq_fillHeader(char* header, char *fieldDelim, fastaSeqPtr seqElem);
fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC);
int32_t seq_findSeqByAccId (char *accid, fastaSeqCountPtr allseqs);
void seq_printSeqs (fastaSeqCountPtr allseq);
int cleanDB(fastaSeqCount);
void addCounts(fastaSeqCount* db);
int uniqSeqsVector(fastaSeqCount* db, fastaSeqPtr** uniqSeqs);
void calculateMaxAndMinLen(fastaSeqPtr* db, int n, int* lmax, int* lmin);
void calculateMaxAndMinLenDB(fastaSeqCount db, int* lmax, int* lmin);
int sortSeqsWithCounts(const void **s1, const void **s2);
int reverseSortSeqsWithCounts(const void **s1, const void **s2);
void readSampleCounts(fastaSeqCount* db, char* key_name);
#endif /*SEQUENCE_H_*/
|
