C++ Fasta file reader

Usage

#include "FastaReader.hpp" 

FastaReader fr("file.fasta"); 
while(fr.hasNextSequence()) 
{ 
   fr.readSequence();
   std::string seq = fr.Sequence();         
   // sequence manipulation 
}

Sequences (fasta record) are read one at a time to limit memory usage. Non alphabetical characters present in the sequences are ignored (e.g space , tabs, ...) .

Fasta file format

>id description
ACGTN
>id description
ACCCC

• https://en.wikipedia.org/wiki/FASTA_format

Fasta command line utilities

# bin/fastatools.exe -h

 fastatools - fasta file utilities
 ----------------------------------
 USAGE:
 
 count - Print nucleotide count (A,C,G,T,N):
    fastatools -c count -f sequence.fa

 head  - Print the first n sequences of a fasta file:
    fastatools -c head  -f sequence.fa  -n number_of_sequence_to_print

 stats - Print sequence stats (# bp, % masked):
    fastatools -c stats -f sequence.fa

Build with cmake

Visual Studio

mkdir build
cd build
cmake ..
cmake --build . --config Release

copy /Y cppunit-src\bin\Release\cppunit.dll ..\test\
copy /Y bin\Release\*.exe ..\test\

cd ..

cd test
Test_cppunit
Test_fastareader
Test_utils 

#...
Unit test for FastaReader class
=========================
FastaReaderTestCase::fastafile : OK
FastaReaderTestCase::fastafile_donotexist : OK
FastaReaderTestCase::fastafile_directory : OK
=========================

Linux

mkdir build
cd build
cmake ..
make

ctest

 Test project /home/jenkins/workspace/FastaReader/build
     Start 1: Test_cppunit
 1/3 Test #1: Test_cppunit .....................   Passed    0.00 sec
     Start 2: Test_fastareader
 2/3 Test #2: Test_fastareader .................   Passed    0.00 sec
     Start 3: Test_utils
 3/3 Test #3: Test_utils .......................   Passed    0.00 sec

Generate Perl, Python or Java bindings with SWIG

perl

 cmake .. -DSWIG_PERL=ON
 cmake .. -DSWIG_PERL=ON -DPERL_EXECUTABLE=/path/perl -DSWIG_EXECUTABLE=/path/swig

• See Perl/swig_perl.md

python

 cmake .. -DSWIG_PYTHON=ON

• See Python/swig_python.md

java

 cmake .. -DSWIG_JAVA=ON

• See Java/swig_java.md

Limitation

The maximum size of a sequence is the size of a std::string (std::size_t) .

Author

David Laperriere [email protected]