File size: 5,178 Bytes
4559903 | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | /*
Bare-bones sequence alignment resampling. Default is bootstrap, alternative is jackknife.
Conserved-partition bootstrap now implemented.
*/
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <cstring>
#include <getopt.h>
#include "utils.h"
#include "sequence.h"
#include "seq_reader.h"
#include "seq_sample.h"
#include "log.h"
#include "citations.h"
void print_help ();
std::string get_version_line ();
void print_help () {
std::cout << std::endl;
std::cout << "Sequence alignment bootstrap or jackknife resampling." << std::endl;
std::cout << "This will take fasta, fastq, phylip, and nexus formats from a file or STDIN." << std::endl;
std::cout << std::endl;
std::cout << "Usage: pxboot [OPTIONS]..." << std::endl;
std::cout << std::endl;
std::cout << "Options:" << std::endl;
std::cout << " -s, --seqf=FILE input sequence file, STDIN otherwise" << std::endl;
std::cout << " -p, --partf=FILE file listing empirical partitions: NAME = START-STOP[\\INTERVAL]" << std::endl;
std::cout << " -f, --frac=DOUBLE jackknife percentage, default bootstrap (i.e. -f 1.0)" << std::endl;
std::cout << " -x, --seed=INT random number seed, clock otherwise" << std::endl;
std::cout << " -o, --outf=FILE output sequence file, STOUT otherwise" << std::endl;
std::cout << " -h, --help display this help and exit" << std::endl;
std::cout << " -V, --version display version and exit" << std::endl;
std::cout << " -C, --citation display phyx citation and exit" << std::endl;
std::cout << std::endl;
std::cout << "Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>" << std::endl;
std::cout << "phyx home page: <https://github.com/FePhyFoFum/phyx>" << std::endl;
}
std::string get_version_line () {
std::string vl = "pxboot 1.3\n";
vl += "Copyright (C) 2013-2021 FePhyFoFum\n";
vl += "License GPLv3\n";
vl += "Written by Joseph W. Brown";
return vl;
}
static struct option const long_options[] =
{
{"seqf", required_argument, nullptr, 's'},
{"outf", required_argument, nullptr, 'o'},
{"partf", required_argument, nullptr, 'p'},
{"frac", required_argument, nullptr, 'f'},
{"seed", required_argument, nullptr, 'x'},
{"help", no_argument, nullptr, 'h'},
{"version", no_argument, nullptr, 'V'},
{"citation", no_argument, nullptr, 'C'},
{nullptr, 0, nullptr, 0}
};
int main(int argc, char * argv[]) {
log_call(argc, argv);
bool outfileset = false;
bool fileset = false;
bool partitioned = false;
double jackfract = 0.0;
char * outf = nullptr;
char * seqf = nullptr;
std::string partf;
long int seed = -1;
while (true) {
int oi = -1;
int c = getopt_long(argc, argv, "s:o:p:f:x:hVC", long_options, &oi);
if (c == -1) {
break;
}
switch(c) {
case 's':
fileset = true;
seqf = strdup(optarg);
check_file_exists(seqf);
break;
case 'o':
outfileset = true;
outf = strdup(optarg);
break;
case 'p':
partitioned = true;
partf = strdup(optarg);
break;
case 'f':
jackfract = string_to_double(optarg, "-f");
if (jackfract < 0 || jackfract > 1) {
std::cerr << "Error: jackknife fraction must be 0 < x < 1. Exiting." << std::endl;
exit(0);
}
break;
case 'x':
seed = string_to_long_int(optarg, "-x");
break;
case 'h':
print_help();
exit(0);
case 'V':
std::cout << get_version_line() << std::endl;
exit(0);
case 'C':
std::cout << get_phyx_citation() << std::endl;
exit(0);
default:
print_error(*argv);
exit(0);
}
}
if (fileset && outfileset) {
check_inout_streams_identical(seqf, outf);
}
std::istream * pios = nullptr;
std::ostream * poos = nullptr;
std::ifstream * fstr = nullptr;
std::ofstream * ofstr = nullptr;
if (outfileset) {
ofstr = new std::ofstream(outf);
poos = ofstr;
} else {
poos = &std::cout;
}
if (fileset) {
fstr = new std::ifstream(seqf);
pios = fstr;
} else {
pios = &std::cin;
if (!check_for_input_to_stream()) {
print_help();
exit(1);
}
}
if (partitioned && (jackfract != 0.0)) {
std::cerr << "Error: partitioned jackknife not implemented. Exiting." << std::endl;
exit(0);
}
SequenceSampler ss(pios, seed, jackfract, partf);
ss.write_resampled_seqs(poos);
if (fileset) {
fstr->close();
delete pios;
}
if (outfileset) {
ofstr->close();
delete poos;
}
return EXIT_SUCCESS;
}
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