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
|
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>
#include <seqan/arg_parse.h>
using namespace seqan;
// ==========================================================================
// Classes
// ==========================================================================
// --------------------------------------------------------------------------
// Class KnimeNodeOptions
// --------------------------------------------------------------------------
// This struct stores the options from the command line.
//
// You might want to rename this to reflect the name of your app.
struct KnimeNodeOptions
{
// Verbosity level. 0 -- quiet, 1 -- normal, 2 -- verbose, 3 -- very verbose.
int verbosity;
// The arguments of the program are stored here.
CharString inputFile;
CharString outputFile;
KnimeNodeOptions() :
verbosity(1)
{}
};
// ==========================================================================
// Functions
// ==========================================================================
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
ArgumentParser::ParseResult
parseCommandLine(KnimeNodeOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
ArgumentParser parser("knime_node");
// Set short description, version, and date.
setShortDescription(parser, "This is a very simple KNIME node providing an input and output port.");
setVersion(parser, "0.1");
setDate(parser, "Sep 2013");
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \"\\fITEXT\\fP\"");
addDescription(parser, "This is a very simple KNIME node providing an input and output port. The code should be modified such that the node does something useful");
// We require one argument.
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "IN"));
setValidValues(parser, 0, SeqFileIn::getFileExtensions());
addOption(parser, ArgParseOption("o", "outputFile", "Name of the multi-FASTA output.", ArgParseOption::OUTPUT_FILE, "OUT"));
setValidValues(parser, "outputFile", SeqFileOut::getFileExtensions());
setDefaultValue(parser, "outputFile", "result.fastq");
// The verbosity option should be used to help debugging
addOption(parser, ArgParseOption("q", "quiet", "Set verbosity to a minimum."));
addOption(parser, ArgParseOption("v", "verbose", "Enable verbose output."));
addOption(parser, ArgParseOption("vv", "very-verbose", "Enable very verbose output."));
// Add Examples Section.
addTextSection(parser, "Examples");
addListItem(parser, "\\fBknime_node\\fP \\fB-v\\fP \\fItext\\fP",
"Call with \\fITEXT\\fP set to \"text\" with verbose output.");
// Parse command line.
ArgumentParser::ParseResult res = parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != ArgumentParser::PARSE_OK)
return res;
// Extract option values.
if (isSet(parser, "quiet"))
options.verbosity = 0;
if (isSet(parser, "verbose"))
options.verbosity = 2;
if (isSet(parser, "very-verbose"))
options.verbosity = 3;
getArgumentValue(options.inputFile, parser, 0);
// Get output file name from command line if set. Otherwise, autogenerate from input file name.
if (isSet(parser, "outputFile"))
{
getOptionValue(options.outputFile, parser, "outputFile");
}
else
{
options.outputFile = options.inputFile;
append(options.outputFile, ".fastq");
}
return ArgumentParser::PARSE_OK;
}
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
ArgumentParser parser;
KnimeNodeOptions options;
ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
if (res != ArgumentParser::PARSE_OK)
return res == ArgumentParser::PARSE_ERROR;
std::cout << "EXAMPLE PROGRAM\n"
<< "===============\n\n";
// Print the command line arguments back to the user.
if (options.verbosity > 0)
{
std::cout << "__OPTIONS____________________________________________________________________\n"
<< '\n'
<< "VERBOSITY\t" << options.verbosity << '\n'
<< "INPUT_FILE\t" << options.inputFile << "\n\n"
<< "OUTPUT_FILE\t" << options.outputFile << "\n\n";
}
// Reading the input
SeqFileIn seqIn(toCString(options.inputFile));
StringSet<CharString> ids;
StringSet<Dna5String> seqs;
StringSet<CharString> quals;
if (atEnd(seqIn))
{
std::cout << "ERROR: File does not contain any sequences!\n";
return 1;
}
readRecords(ids, seqs, quals, seqIn);
// DO SOMETHING HERE
// *
// *
// *
SeqFileOut seqOut(toCString(options.outputFile));
writeRecords(seqOut, ids, seqs, quals);
return 0;
}
|