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    copied!<p>If those are variable numbers of "regions" and variable numbers of file name strings you could make your life easier by using vectors instead of arrays.</p> <p>And in general, I wouldn't do something like this in C++, but rather Python, Ruby, etc. C++ is really not made for such tasks... Anyway, here is some quick and dirty code that should do the job. You can clean it up by refactoring...</p> <pre><code>#include &lt;iostream&gt; #include &lt;string&gt; #include &lt;fstream&gt; #include &lt;sstream&gt; #include &lt;vector&gt; #include &lt;numeric&gt; #include &lt;algorithm&gt; using std::vector; using std::cout; using std::cin; using std::endl; using std::string; using std::ifstream; using std::istringstream; void split(const string &amp;s, vector&lt;string&gt; &amp;elems, char sep=' ') { string element = ""; vector&lt;string&gt; splitted_ints; for (auto c : s) { if (c != sep) element.push_back(c); else { elems.push_back(element); element = ""; } // end if } // end for loop if (element != "") elems.push_back(element); } // end split() int main() { string line; vector&lt;string&gt; first_line; vector&lt;string&gt; second_line; vector&lt;string&gt; splitted_ints; vector&lt;int&gt; from; vector&lt;int&gt; to; vector&lt;string&gt; filenames; ifstream in_file("input.txt"); getline(in_file, line); split(line, first_line, ' '); getline(in_file, line); split(line, second_line, ' '); for (string ele : first_line) split(ele, splitted_ints, ':'); // now you have the integer sequence of the first line // in splitted_ints, e.g., 48, 49, 68, 70, 93, 100 size_t i = 0; while (i &lt; splitted_ints.size()){ int num; istringstream (splitted_ints[i]) &gt;&gt; num; from.push_back(num); ++i; istringstream (splitted_ints[i]) &gt;&gt; num; to.push_back(num); ++i; } splitted_ints.clear(); // repeat for second line for (string ele : second_line) split(ele, splitted_ints, ':'); i = 0; while (i &lt; splitted_ints.size()){ int num; istringstream (splitted_ints[i]) &gt;&gt; num; from.push_back(num); ++i; istringstream (splitted_ints[i]) &gt;&gt; num; to.push_back(num); ++i; } // append the rest of the input file (i.e., the filenames) while (getline(in_file, line)) { filenames.push_back(line); } </code></pre> <p>// Printing out the contents to make sure it worked</p> <pre><code> cout &lt;&lt; "FILENAMES:\n"; for (auto ele : filenames) cout &lt;&lt; ele &lt;&lt; ","; cout &lt;&lt; "\nFROM numbers:\n"; for (auto ele : from) cout &lt;&lt; ele &lt;&lt; ","; cout &lt;&lt; "\nTO numbers:\n"; for (auto ele : to) cout &lt;&lt; ele &lt;&lt; ","; cout &lt;&lt; endl; /* FILENAMES: tr429a.frank/tr429a.reg1.0.pdb ,tr429a.frank/tr429a.reg1.1.pdb ,tr429a.frank/tr429a.reg1.2.pdb ,tr429a.frank/tr429a.reg1.3.pdb ,tr429a.frank/tr429a.reg1.4.pdb ,tr429a.frank/tr429a.reg1.5.pdb ,tr429a.frank/tr429a.reg1.6.pdb ,tr429a.frank/tr429a.reg1.7.pdb, FROM numbers: 48,68,93,22,34,50,71, TO numbers: 49,70,100,33,47,67,92, */ return 0; } </code></pre>
 

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