Easel (pyhmmer.easel)

High-level interface to the Easel C library.

Easel is a library developed by the Eddy/Rivas Lab to facilitate the development of biological software in C. It is used by HMMER and Infernal.

Data Structures

Bitfield	A statically sized sequence of booleans stored as a packed bitfield.
KeyHash	A dynamically resized container to store byte keys using a hash table.

Sequences

Sequence	An abstract biological sequence with some associated metadata.
TextSequence	A biological sequence stored in text mode.
DigitalSequence	A biological sequence stored in digital mode.

Sequence Blocks

SequenceBlock	An abstract container for storing Sequence objects.
TextSequenceBlock	A container for storing TextSequence objects.
DigitalSequenceBlock	A container for storing DigitalSequence objects.

Alignments

MSA	An abstract alignment of multiple sequences.
TextMSA	A multiple sequence alignement stored in text mode.
DigitalMSA	A multiple sequence alignment stored in digital mode.

Parsers

SequenceFile	A wrapper around a sequence file, containing unaligned sequences.
MSAFile	A wrapper around a multiple-alignment file.

Linear Algebra

Vector	An abstract 1D array of fixed size.
VectorF	A vector storing single-precision floating point numbers.
VectorU8	A vector storing byte-sized unsigned integers.
Matrix	An abstract 2D array of fixed size.
MatrixF	A matrix storing single-precision floating point numbers.
MatrixU8	A matrix storing byte-sized unsigned integers.

Miscellaneous

Alphabet	A biological alphabet, including additional marker symbols.
GeneticCode	A genetic code table for translation.
Randomness	A portable, thread-safe random number generator.
SSIReader	A read-only handler for sequence/subsequence index file.
SSIWriter	A writer for sequence/subsequence index files.