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// ==========================================================================
// SeqCons
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
#include "seqcons_options.h"
namespace { // anonymous namespace
// --------------------------------------------------------------------------
// Function strToMethod()
// --------------------------------------------------------------------------
SeqConsOptions::Operation strToMethod(std::string opStr)
{
if (opStr == "align_consensus")
return SeqConsOptions::ALN_CONSENSUS;
else if (opStr == "overlap_consensus")
return SeqConsOptions::OVL_CONSENSUS;
else if (opStr == "contig_consensus")
return SeqConsOptions::CTG_CONSENSUS;
else if (opStr == "pos_consensus")
return SeqConsOptions::POS_CONSENSUS;
else if (opStr == "realign")
return SeqConsOptions::REALIGN;
else // opStr == "nop"
return SeqConsOptions::NOP;
}
// --------------------------------------------------------------------------
// Function operationStr()
// --------------------------------------------------------------------------
char const * operationStr(SeqConsOptions::Operation op)
{
static char const * labels[] = {
"convert only",
"realign only",
"consensus with positions",
"contig-wise MSA + consensus",
"overlap MSA + consensus",
"global MSA + consensus"
};
return labels[op];
}
// --------------------------------------------------------------------------
// Function verbosityStr()
// --------------------------------------------------------------------------
char const * verbosityStr(int verbosity)
{
static char const * labels[] = {
"QUIET",
"NORMAL",
"VERBOSE",
"VERY VERBOSE"
};
verbosity = std::max(std::min(verbosity, 3), 0);
return labels[verbosity];
}
} // anonymous namespace
// --------------------------------------------------------------------------
// Class SeqConsOptions
// --------------------------------------------------------------------------
void SeqConsOptions::checkConsistency()
{
// Position information is only available when input is in SAM format and is required for
// position-/contig-based consensus and realignment.
seqan::CharString inFileLowerCase = inputFile;
seqan::toLower(inFileLowerCase);
if ((operation == POS_CONSENSUS || operation == CTG_CONSENSUS || operation == REALIGN) &&
(!endsWith(inFileLowerCase, ".sam")))
throw std::runtime_error("SAM input required for coordinates. Either specify SAM file for the "
"input or use \"--method overlap_consensus\" or \"--method align_consensus\".");
}
void SeqConsOptions::print(std::ostream & out) const
{
out << "VERBOSITY \t" << verbosityStr(verbosity) << "\n"
<< "OPERATION \t" << operationStr(operation) << "\n"
<< "\n"
<< "INPUT FILE \t" << inputFile << "\n"
<< "OUTPUT READS \t" << outputFileAlignment << "\n"
<< "OUTPUT CONSENSUS \t" << outputFileConsensus << "\n"
<< "\n"
<< "OVERLAP MIN LENGTH \t" << overlapMinLength << "\n"
<< "OVERLAP MAX ERR-RATE \t" << overlapMaxErrorRate << "\n"
<< "OVERLAP MIN COUNT \t" << overlapMinCount << "\n"
<< "OVERLAP WINDOW SIZE \t" << overlapWindowSize << "\n"
<< "\n"
<< "K-MER SIZE \t" << kMerSize << "\n"
<< "K-MER MAX OCCURRENCES \t" << kMerMaxOcc << "\n"
<< "\n"
<< "REALIGNMENT BANDWIDTH \t" << reAlignmentBandwidth << "\n"
<< "REALIGNMENT ENVIRONMENT\t" << reAlignmentEnvironment << "\n";
}
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
seqan::ArgumentParser::ParseResult
parseCommandLine(SeqConsOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
seqan::ArgumentParser parser("seqcons2");
// Set short description, version, and date.
setShortDescription(parser, "Compute consensus from sequences.");
setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
setDate(parser, SEQAN_DATE);
// Define usage line and long description.
addUsageLine(parser,
"\\fB-i\\fP \\fIINPUT.{fa,sam}\\fP [\\fB-oa\\fP \\fIOUT_ALIGN.{fa,sam}\\fP] "
"[\\fB-oc\\fP \\fIOUT_CONSENSUS.fa\\fP]");
addDescription(parser,
"Compute consensus from sequences with and without approximate alignment information.");
// Overall Program Options
addOption(parser, seqan::ArgParseOption("q", "quiet", "Set verbosity to a minimum."));
addOption(parser, seqan::ArgParseOption("v", "verbose", "Enable verbose output."));
addOption(parser, seqan::ArgParseOption("vv", "very-verbose", "Enable very verbose output."));
addOption(parser, seqan::ArgParseOption("m", "method", "Method to perform. See section \\fIMethods\\fP "
"below for details.", seqan::ArgParseOption::STRING, "METHOD"));
setValidValues(parser, "method", "nop realign align_consensus overlap_consensus contig_consensus pos_consensus");
setDefaultValue(parser, "method", "pos_consensus");
// I/O Options
addSection(parser, "I/O Options");
addOption(parser, seqan::ArgParseOption("i", "input-file", "Input file.", seqan::ArgParseOption::INPUT_FILE,
"INPUT"));
setRequired(parser, "input-file", true);
setValidValues(parser, "input-file", "sam fa fasta");
addOption(parser, seqan::ArgParseOption("oa", "output-alignment-file", "Output file with alignment.",
seqan::ArgParseOption::OUTPUT_FILE, "OUT_ALIGNMENT"));
setRequired(parser, "output-alignment-file", false);
setValidValues(parser, "output-alignment-file", "sam txt");
addOption(parser, seqan::ArgParseOption("oc", "output-consensus-file", "Output file with consensus sequence.",
seqan::ArgParseOption::OUTPUT_FILE, "OUT_CONSENSUS"));
setRequired(parser, "output-consensus-file", false);
setValidValues(parser, "output-consensus-file", "fa fasta");
// Alignment Quality Filter Options
addSection(parser, "Alignment Quality Filter Options");
addOption(parser, seqan::ArgParseOption("", "overlap-min-length", "Minimal overlap length.",
seqan::ArgParseOption::INTEGER, "LENGTH"));
setMinValue(parser, "overlap-min-length", "0");
setDefaultValue(parser, "overlap-min-length", "20");
addOption(parser, seqan::ArgParseOption("", "overlap-max-error", "Maximal error rate in overlap as percentage.",
seqan::ArgParseOption::DOUBLE, "RATE"));
setMinValue(parser, "overlap-max-error", "0.0");
setDefaultValue(parser, "overlap-max-error", "5.0");
addOption(parser, seqan::ArgParseOption("", "overlap-min-count", "Minimal overlap count.",
seqan::ArgParseOption::INTEGER, "COUNT"));
setMinValue(parser, "overlap-min-count", "0");
setDefaultValue(parser, "overlap-min-count", "3");
addOption(parser, seqan::ArgParseOption("", "overlap-window-size", "Window size to look for alignments.",
seqan::ArgParseOption::INTEGER, "SIZE"));
setMinValue(parser, "overlap-window-size", "0");
setDefaultValue(parser, "overlap-window-size", "20");
// K-mer Filter Options
addSection(parser, "K-Mer Filter Options");
addOption(parser, seqan::ArgParseOption("", "k-mer-size", "The k-mer size to use.",
seqan::ArgParseOption::INTEGER, "LENGTH"));
setMinValue(parser, "k-mer-size", "5");
setDefaultValue(parser, "k-mer-size", "20");
addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore k-mer with higher occurrence count, 0 to disable.",
seqan::ArgParseOption::INTEGER, "COUNT"));
setMinValue(parser, "k-mer-max-occ", "0");
setDefaultValue(parser, "k-mer-max-occ", "200");
// Realignment Options
addSection(parser, "Realignment Options");
addOption(parser, seqan::ArgParseOption("", "realign-bandwidth",
"Bandwidth to use for pairwise alignments in realignment.",
seqan::ArgParseOption::INTEGER, "LENGTH"));
setMinValue(parser, "realign-bandwidth", "5");
setDefaultValue(parser, "realign-bandwidth", "10");
addOption(parser, seqan::ArgParseOption("", "realign-environment",
"Environment for extraction in realignment.",
seqan::ArgParseOption::INTEGER, "COUNT"));
setMinValue(parser, "realign-environment", "5");
setDefaultValue(parser, "realign-environment", "20");
// Add Methods Section
addTextSection(parser, "Methods");
addListItem(parser, "\\fBnop\\fP",
"Perform no action, just perform file conversion if possible.");
addListItem(parser, "\\fBrealign\\fP",
"Perform realignment, requires input to be a SAM file to provide approximate position "
"information, creates consensus sequence after realignment.");
addListItem(parser, "\\fBoverlap_consensus\\fP",
"Perform MSA with overlap alignments of the input ignoring any given coordinates, then realign. "
"This is most suited when computing the consensus of reads where the underlying sequence is very "
"similar and most differences stem from sequencing errors and not genomic variation. All "
"pairwise alignments computed here are banded.");
addListItem(parser, "\\fBalign_consensus\\fP",
"Perform MSA with global alignments of the input ignoring any given coordinates, then realign. "
"This will computed unbanded global ends-gap free pairwise alignments. This is also suitable "
"when aligning different sequences, e.g. clustered transcripts. Using this method, seqcons "
"will be similar to calling SeqAn::T-Coffee, followed by realignment and consensus computation.");
addListItem(parser, "\\fBcontig_consensus\\fP",
"Perform MSA of the input, contig by contig, requires contig information, then realign. Input "
"must be SAM.");
addListItem(parser, "\\fBpos_consensus\\fP",
"Perform consensus of the input, then realign. Requires approximate coordinate information in "
"SAM file.");
// Add Output Section
addTextSection(parser, "Output Formats");
addText(parser,
"The program can write out the consensus sequence in FASTA format and optionally the alignment of the "
"input sequences against the consensus in SAM/BAM format. When using the extension \\fI.txt\\fP, seqcons "
"will write out the MSA as a plain text visualization.");
// Add Examples Section
addTextSection(parser, "Examples");
addListItem(parser,
"\\fBseqcons\\fP \\fB-m\\fP \\fIovl_consensus\\fP \\fB-i\\fP \\fIreads.fa\\fP \\fB-oa\\fP "
"\\fIout.sam\\fP \\fB-oc\\fP \\fIcons.fa\\fP",
"Compute MSA of the sequences in \\fIreads.fa\\fP. The consensus sequence is written to "
"\\fIcons.fa\\fP and the alignment of the sequences in \\fIreads.fa\\fP is written to "
"\\fIout.sam\\fP.");
addListItem(parser,
"\\fBseqcons\\fP \\fB-m\\fP \\fIrealign\\fP \\fB-i\\fP \\fIin.sam\\fP \\fB-oa\\fP \\fIout.sam\\fP",
"Read in multi-read alignment from \\fIin.sam\\fP, refine it using Anson-Myers realignment and "
"write out the refined alignment to \\fIout.sam\\fP");
// 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;
// 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;
std::string opStr;
getOptionValue(opStr, parser, "method");
options.operation = strToMethod(opStr.c_str());
getOptionValue(options.inputFile, parser, "input-file");
getOptionValue(options.outputFileAlignment, parser, "output-alignment-file");
getOptionValue(options.outputFileConsensus, parser, "output-consensus-file");
getOptionValue(options.overlapMinLength, parser, "overlap-min-length");
getOptionValue(options.overlapMaxErrorRate, parser, "overlap-max-error");
getOptionValue(options.overlapWindowSize, parser, "overlap-window-size");
getOptionValue(options.kMerSize, parser, "k-mer-size");
getOptionValue(options.kMerMaxOcc, parser, "k-mer-max-occ");
getOptionValue(options.reAlignmentBandwidth, parser, "realign-bandwidth");
getOptionValue(options.reAlignmentEnvironment, parser, "realign-environment");
return seqan::ArgumentParser::PARSE_OK;
}
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