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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007-2012
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
==========================================================================*/
#include "lib/pair_align_lib.h"
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
seqan::ArgumentParser::ParseResult
parseCommandLine(Options & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
seqan::ArgumentParser parser("pair_align");
// Set short description, version, and date.
setShortDescription(parser, "Pairwise alignment");
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
setDate(parser, SEQAN_DATE);
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-s\\fP \\fIIN\\fP");
setCategory(parser, "Sequence Alignment");
addDescription(parser,
"The program allows one to align two sequences using dyamic programming alignment algorithms while "
"tweaking various parameters.");
addSection(parser, "Main Options");
addOption(parser, seqan::ArgParseOption("s", "seq", "FASTA file with two sequences.", seqan::ArgParseOption::INPUT_FILE, "IN"));
setRequired(parser, "seq");
setValidValues(parser, "seq", getFileExtensions(Fasta()));
addOption(parser, seqan::ArgParseOption("a", "alphabet", "Sequence alphabet.", seqan::ArgParseOption::STRING, "ALPHABET"));
setValidValues(parser, "alphabet", "protein dna rna text");
setDefaultValue(parser, "alphabet", "protein");
addOption(parser, seqan::ArgParseOption("m", "method",
"DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, "
"Longest Common Subsequence",
seqan::ArgParseOption::STRING, "METHOD"));
setValidValues(parser, "method", "nw gotoh sw lcs");
setDefaultValue(parser, "method", "gotoh");
addOption(parser, seqan::ArgParseOption("o", "outfile", "Output filename.", seqan::ArgParseOption::OUTPUT_FILE, "OUT"));
setDefaultValue(parser, "outfile", "out.fasta");
std::vector<std::string> outFileNames = getFileExtensions(Fasta());
outFileNames.push_back(".msf");
setValidValues(parser, "outfile", outFileNames);
addSection(parser, "Scoring Options");
addOption(parser, seqan::ArgParseOption("g", "gop", "Gap open penalty.", seqan::ArgParseOption::INTEGER, "INT"));
setDefaultValue(parser, "gop", "-11");
addOption(parser, seqan::ArgParseOption("e", "gex", "Gap extension penalty.", seqan::ArgParseOption::INTEGER, "INT"));
setDefaultValue(parser, "gex", "-1");
addOption(parser, seqan::ArgParseOption("ma", "matrix", "Score matrix.", seqan::ArgParseOption::STRING, "MATRIX_FILE"));
addOption(parser, seqan::ArgParseOption("ms", "msc", "Match score.", seqan::ArgParseOption::INTEGER, "INT"));
setDefaultValue(parser, "msc", "5");
addOption(parser, seqan::ArgParseOption("mm", "mmsc", "Mismatch penalty.", seqan::ArgParseOption::INTEGER, "INT"));
setDefaultValue(parser, "mmsc", "-4");
addSection(parser, "Banded Alignment Options");
addOption(parser, seqan::ArgParseOption("lo", "low", "Lower diagonal.", seqan::ArgParseOption::INTEGER, "INT"));
addOption(parser, seqan::ArgParseOption("hi", "high", "Upper diagonal.", seqan::ArgParseOption::INTEGER, "INT"));
addSection(parser, "DP Matrix Configuration Options");
addOption(parser, seqan::ArgParseOption("c", "config", "Alignment configuration.", seqan::ArgParseOption::STRING, "CONF"));
setValidValues(parser, "config", "ffff ffft fftf fftt ftff ftft fttf fttt tfff tfft tftf tftt ttff ttft tttf tttt");
addTextSection(parser, "Alignment configuration");
addText(parser,
"The alignment configuration is a string of four characters, each being either t or f. All "
"combinations are allowed. The meaning is as follows.");
addListItem(parser, "tfff", "First row initialized with 0s.");
addListItem(parser, "ftff", "First column initialized with 0s.");
addListItem(parser, "fftf", "Search last column for maximum.");
addListItem(parser, "ffft", "Search last row for maximum.");
// Parse command line.
seqan::ArgumentParser::ParseResult res = seqan::parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != seqan::ArgumentParser::PARSE_OK)
return res;
getOptionValue(options.inputFile, parser, "seq");
getOptionValue(options.outputFile, parser, "outfile");
getOptionValue(options.alphabet, parser, "alphabet");
getOptionValue(options.method, parser, "method");
//getOptionValue(options.format, parser, "format");
getOptionValue(options.gop, parser, "gop");
getOptionValue(options.gex, parser, "gex");
getOptionValue(options.matrix, parser, "matrix");
getOptionValue(options.msc, parser, "msc");
getOptionValue(options.mmsc, parser, "mmsc");
getOptionValue(options.low, parser, "low");
getOptionValue(options.high, parser, "high");
getOptionValue(options.config, parser, "config");
return seqan::ArgumentParser::PARSE_OK;
}
int main(int argc, const char* argv[])
{
// Parse the command line.
Options options;
seqan::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 != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
// Defer to the library code pair_align_lib.a.
// For every major alignment configuration there is a single translation unit
// breaking down the compiled source code to single sources. This reduces the
// memory needed for the compilation to some MB. Note before it were several GB.
// Also the library can built in parallel which also speeds up the compilation
// process.
pairAlignMain(options);
return res;
}
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