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
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
|
#include <iostream>
#include <cstdlib>
#include <fstream>
#include <string>
#include <map>
#include <algorithm>
#include "fasta.hpp"
#include <boost/program_options.hpp>
namespace po = boost::program_options;
template <class InputIterator>
std::string firstWord(InputIterator first, InputIterator last)
{
return std::string(first, std::find_if(first, last, isspace));
}
int main(int argc, char *argv[])
{
bool produce_help;
bool cluster_centers;
bool all_clusters;
bool everything_except;
bool cluster_sequences;
std::string fasta_file_name;
std::string clusters_file_name_prefix;
const std::string FASTA_SUFFIX = "fasta";
po::options_description desc("Options");
desc.add_options()
("help,h", po::bool_switch(&produce_help), "Produce help message.")
("fasta-file,f", po::value<std::string>(&fasta_file_name), "REQUIRED - File containing sequences in FASTA format.")
("cluster-centers,c", po::bool_switch(&cluster_centers), "Write the sequences of all cluster centers to standard output in FASTA format.")
("all-clusters,a", po::bool_switch(&all_clusters), "Write the sequences of each cluster to a seperate FASTA file. The name of the files will be the given path and prefix, folloed by cluster number andy a \'.fasta\' suffix.")
("file-name-prefix,p", po::value<std::string>(&clusters_file_name_prefix)->default_value("./cluster-"), "Specify the path and prefix for the cluster FASTA file names.")
("everything-except", po::bool_switch(&everything_except), "Write all sequences except cluster centers to the standard output in FASTA format.")
("cluster-sequences", po::bool_switch(&cluster_sequences), "Write the cluster sequences (but not the cluster center sequence) to the standard output in FASTA format.")
;
po::variables_map vm;
po::store(po::command_line_parser(argc, argv).options(desc).run(), vm);
notify(vm);
if (produce_help || fasta_file_name.empty()) {
std::cerr << "Usage: fastaselect FastaFile\n"
<< " The ids are read from standard input. Each line corresponds to a cluster with the first id being the cluster center.\n"
<< " The output sequences are written to standard output in FASTA format.\n"
<< desc << '\n';
exit(EXIT_FAILURE);
}
std::ifstream fasta_file(fasta_file_name.c_str());
sequence::Fasta sequences;
fasta_file >> sequences;
typedef std::map<std::string, size_t> StringIndexMap;
StringIndexMap index_of_id;
for (size_t i = 0; i < sequences.size(); ++i) {
const std::string &header = sequences[i].header;
index_of_id[firstWord(header.begin(), header.end())] = i;
}
if (cluster_centers) {
std::string line;
while (getline(std::cin, line)) {
std::string center_id = firstWord(line.begin(), line.end());
std::cout << sequences[index_of_id[center_id]];
}
} else if (everything_except) {
std::set<std::string> center_ids;
{
std::string line;
while (getline(std::cin, line))
center_ids.insert(firstWord(line.begin(), line.end()));
}
for (size_t i = 0; i < sequences.size(); ++i) {
const std::string &header = sequences[i].header;
std::string id = firstWord(header.begin(), header.end());
if (center_ids.find(id) == center_ids.end())
std::cout << sequences[i];
}
} else if (cluster_sequences) {
std::string line;
while (getline(std::cin, line)) {
std::istringstream line_stream(line);
std::string id;
line_stream >> id;
while (line_stream >> id)
std::cout << sequences[index_of_id[id]];
}
}
if (all_clusters) {
std::string line;
int cluster_number = 0;
while (getline(std::cin, line)) {
std::ostringstream cluster_file_name_stream;
cluster_file_name_stream << clusters_file_name_prefix << ++cluster_number << '.' << FASTA_SUFFIX;
std::ofstream cluster_file(cluster_file_name_stream.str().c_str());
std::istringstream line_stream(line);
std::string id;
while (line_stream >> id)
cluster_file << sequences[index_of_id[id]];
}
}
return EXIT_SUCCESS;
}
|
