This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Multi-Fasta Sequence Input C++ Library

Hi, I am new to bioinformatics and I was wondering if there is any C++ library for efficiently reading and indexing multi-fasta file?

fasta library
• 6,767 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Lexxx233 • Lexxx233

What do you mean by "indexing" ? Do you mean what "samtools faidx" does ?

• 0 views • link
written by Gabriel R. Gabriel R.

2 answers

"efficiently .. indexing" is a bit vague, but I guess you will find nice things in seqAn: http://www.seqan.de/

  1. indexing by sequence name and position (like samtools fai): http://trac.seqan.de/wiki/Tutorial/IndexedFastaIO

  2. other indices (suffix tree...): http://trac.seqan.de/wiki/Tutorial/Indices

• 211 views • link
written by Ido Tamir Ido Tamir

I've got something like this in my sources. See:

https://code.google.com/p/variationtoolkit/source/browse/trunk/src/fastareader.cpp

https://code.google.com/p/variationtoolkit/source/browse/trunk/src/fastareader.h

for indexing the sequence, you can use a key/value datastore like leveldb , berkeleydb,.... or a embedded sql database like sqlite etc...

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this