FastaPlus version 0.01
=======================
FULL NAME:
C++ container for Fasta records
DESCRIPTION:
The container is designed to provide a set of easy to use data formatting utilities for (multi)fasta formated files. In addition it facilitates (DNA:to be implemented)AA sequence cleaning strategies like low complexity segment filtering and dubious chrarcter replacment. Moreover, the library enables a unique indexing of individual records based on their taxonnomy identifier as well as particular substring position.
SYNOPSIS:
#include<string>
#include<Fasta>
using namespace fasta;
string myseq("HI MY NAME IS ROBERT and this Is my Sequence!!")
/* Make Fasta object */
/* Construction */
Fasta<int> NewFastaObj(in, taxid);
/* Usage */
cout << "This file contains:" << NewFastaObj.GetObjSummary("TotSeq") << " sequences\n";
cout << "This file contains:" << NewFastaObj.GetObjSummary("TotSeqSize") << " sequence characters\n";
/* Load from inside a program always assumes a clean record */
string id = NewFastaObj.LoadFastaRec("MySeq", myseq, "10001");
unordered_map<string,string> ret = NewFastaObj.GetFastaOnly(id);
cout << "I added this sequence to my container: " << ret[id] << endl;
// prints: HI MY NAME IS ROBERT and this Is my Sequence!!
cout << "My name is: " << NewFastaObj.GetSubStr(id,15,20) << endl;
// prints: ROBERT
cout << "And you can locate my sequence in " << out << "directory under " << id << " ID\n";
// prints --- and 0000000000000000000100016693/0
NewFastaObj.DmpFastaAll(out); // dumps the content to "out" file
NewFastaObj.Clear() // explicite destructor
CONSTRUCTION AND RUNTIME COMPLEXITY:
-
ACKNOWLEDGMENTS:
-
AUTHOR:
Robert Bakaric <rbakaric@irb.hr>, <bakaric@evolbio.mpg.de>
COPYRIGHT AND LICENSE:
* Copyright 2015 Robert Bakaric
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
* MA 02110-1301, USA.