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comparison IMSAME/src/reverseComplement.c @ 0:762009a91895 draft

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author bitlab
date Sat, 15 Dec 2018 18:04:10 -0500
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-1:000000000000 0:762009a91895
1 /* reverseComplement.c
2 Program reading a FASTA file as input (one or multiple sequence)
3 and then returning the reverse complementary sequence in the output file.
4 It is important to note that for multiple sequence file the first input
5 sequence is the last one at the output file and the last one in the input
6 is the first one in the output.
7 oscart@uma.es
8 */
9
10 #include <stdio.h>
11 #include <stdlib.h>
12 #include <string.h>
13 #include <ctype.h>
14 #include <inttypes.h>
15 #include "commonFunctions.h"
16
17 #define SEQSIZE 2000000000
18 #define READINPUT 10000
19 #define WSIZE 32
20 #define NREADS 1000000
21
22 int main(int ac, char** av) {
23 FILE *fIn, *fOut;
24 int64_t i, j, nR, seqLen = 0;
25 char *seq, c, toW;
26 long *offset = NULL;
27
28 if (ac != 3)
29 terror("USE: reverseComplement seqFile.IN reverseComplementarySeq.OUT");
30
31 /**
32 * Allocating memory for the sequence
33 * Fixed amount of memory, change it to loadSeqDB?
34 */
35 if ((seq = (char*) malloc(SEQSIZE)) == NULL)
36 terror("memory for Seq");
37
38 if ((fIn = fopen(av[1], "rt")) == NULL)
39 terror("opening IN sequence FASTA file");
40
41 if ((fOut = fopen(av[2], "wt")) == NULL)
42 terror("opening OUT sequence Words file");
43
44 if ((offset = (long *) malloc(sizeof(long)*NREADS)) == NULL)
45 terror("memory for offsets");
46
47 for(i=0;i<NREADS;i++){
48 offset[i]=0;
49 }
50
51 nR = 0;
52 c = fgetc(fIn);
53 while(!feof(fIn)){
54 if(c == '>'){
55 offset[nR++] = ftell(fIn)-1;
56 }
57 c = fgetc(fIn);
58 }
59
60 for(i=nR-1; i>=0; i--){
61 fseek(fIn, offset[i], SEEK_SET);
62 //READ and write header
63 fgets(seq, READINPUT, fIn);
64
65 fprintf(fOut, "%s", seq);
66 //READ and write sequence
67 c = fgetc(fIn);
68 while(c != '>' && !feof(fIn)){
69 if(isupper(c) || islower(c)){
70 seq[seqLen++]=c;
71 }
72 c = fgetc(fIn);
73 }
74 for(j=seqLen-1; j >= 0; j--){
75 switch(seq[j]){
76 case 'A':
77 toW = 'T';
78 break;
79 case 'C':
80 toW = 'G';
81 break;
82 case 'G':
83 toW = 'C';
84 break;
85 case 'T':
86 toW = 'A';
87 break;
88 case 'U':
89 toW = 'A';
90 break;
91 case 'a':
92 toW = 't';
93 break;
94 case 'c':
95 toW = 'g';
96 break;
97 case 'g':
98 toW = 'c';
99 break;
100 case 't':
101 toW = 'a';
102 break;
103 case 'u':
104 toW = 'a';
105 break;
106 default:
107 toW = seq[j];
108 break;
109 }
110 fwrite(&toW, sizeof(char), 1, fOut);
111 }
112 toW='\n';
113 fwrite(&toW, sizeof(char), 1, fOut);
114 seqLen=0;
115 }
116
117 fclose(fIn);
118 fclose(fOut);
119
120 return 0;
121 }
122
123