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
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
|
// Fasta_to_raw 1.0
// Copyright (C) 2013 Federico Zambelli and Giulio Pavesi
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#include <string>
#include <iostream>
#include <fstream>
#include <vector>
#include <sstream>
#include <math.h>
#include <map>
#include <cstdlib>
using namespace std;
int main(int argc, char **argv)
{
if(argc < 2)
{
cerr << "\nSyntax: fasta_to_raw file1 [file2] ... [fileN]" << endl;
exit(1);
}
// ofstream out("info.txt");
for(unsigned int i = 1; i < argc; i++)
{
ifstream in(argv[i]);
if(!in)
{
cerr << "\nCan't find " << argv[i] << endl;
in.close();
continue;
}
string line;
getline(in,line);
if(line[0] != '>')
{
cerr << "\nBad file format in: " << argv[i] << endl;
in.close();
continue;
}
string fout = line.substr(1).c_str();
for(unsigned int k = 0; k < 3; k++)
fout[k] = tolower(fout[k]);
fout += ".raw";
ofstream out2(fout.c_str());
while(getline(in,line))
{
if(line[0] == '>')
{
out2.close();
fout = line.substr(1).c_str();
for(unsigned int k = 0; k < 3; k++)
fout[k] = tolower(fout[k]);
fout += ".raw";
out2.open((fout.c_str()));
continue;
}
for(unsigned int j = 0; j < line.size(); j++)
{
line[j] = toupper(line[j]);
if(line[j] != 'N' && line[j] != 'A' && line[j] != 'C' && line[j] != 'G' && line[j] != 'T')
line[j] = 'N';
}
out2 << line;
}
out2.close();
in.close();
}
return 0;
}
|
