libsequence  1.9.5
valid_dna.cc
1 
2 #include <Sequence/Fasta.hpp>
5 #include <fstream>
6 #include <iostream>
7 #include <algorithm>
8 
9 int main(int argc, char **argv)
10 {
11  std::ifstream in(argv[1]);
12  Sequence::Fasta seq;
13  while (in >> seq)
14  {
15  std::cout << Sequence::validSeq(seq.begin(),seq.end())
16  << '\t'
18  << '\t'
19  << (std::find_if(seq.begin(),seq.end(),Sequence::ambiguousNucleotide())
20  != seq.end())
21  <<'\n';
22  }
23 }
FASTA sequence stream.
Definition: Fasta.hpp:49
Tests if a character is in the set A,G,C,T.
various useful rexex-based functions for dealing with data. Declares Sequence::basic_dna_alphabet,Sequence::full_dna_alphabet, Sequence::pep_alphabet, and the function Sequence::validSeq.
iterator begin()
Definition: Seq.cc:189
bool validSeq(Iter beg, Iter end, const char *_pattern=Sequence::basic_dna_alphabet, const bool icase=true)
Definition: SeqRegexes.hpp:55
iterator end()
Definition: Seq.cc:198
const char * full_dna_alphabet
Definition: SeqRegexes.hpp:45
Declaration of Sequence::Fasta streams.