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117 lines (90 loc) · 3.31 KB
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// fasta2parts.cpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* Split the sequences a FASTA file into chunks without breaking sequences
*
*/
#undef NDEBUG
#include "common.hpp"
using namespace Common_sp;
#include "common.inc"
namespace
{
struct ThisApplication final : Application
{
ThisApplication ()
: Application ("Split the sequences a FASTA file into parts without breaking sequences")
{
addPositional ("in", "FASTA file");
addPositional ("parts_max", "Max. number of parts (>= 2)");
addPositional ("dir", "Output directory where chunks are saved named by integers starting with 1");
version = SVN_REV;
}
void body () const final
{
const string fName = getArg ("in");
const size_t parts_max = str2<size_t> (getArg ("parts_max"));
const string dirName = getArg ("dir");
if (parts_max <= 1)
throw runtime_error ("Number of parts must be >= 2");
const size_t chunk_min = (size_t) getFileSize (fName) / parts_max + 1;
size_t part = 0;
unique_ptr<OFStream> out;
size_t seqSize = 0;
LineInput f (fName);
while (f. nextLine ())
{
trimTrailing (f. line);
if (f. line. empty ())
continue;
if ( f. line [0] == '>'
&& seqSize >= chunk_min
&& part < parts_max
)
{
out. reset ();
seqSize = 0;
}
if (! out. get ())
{
part++;
ASSERT (part <= parts_max);
out. reset (new OFStream (dirName, toString (part), ""));
}
*out << f. line << endl;
seqSize += f. line. size ();
}
}
};
} // namespace
int main (int argc,
const char* argv[])
{
ThisApplication app;
return app. run (argc, argv);
}