bioforma 0.1.0a0

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🧬 bioforma

Rust-bio wrap for Python. Use the speed of Rust with the Python's high-level for bioinformatics challenges.

Installation

Install using pip install bioforma.

Status

⚠️ In the active development phase. ⚠️

Progress tree (15/92):

• alignment
  • distance.rs
  • pairwise
    • banded.rs
  • poa.rs
  • sparse.rs
• alphabets
  • dna.rs
  • protein.rs
  • rna.rs
• data_structures
  • annot_map.rs
  • bit_tree.rs
  • bitenc.rs
  • bwt.rs
  • fmindex.rs
  • interpolation_table.rs
  • interval_tree
    • array_backed_interval_tree.rs
    • avl_interval_tree.rs
  • qgram_index.rs
  • rank_select.rs
  • smallints.rs
  • suffix_array.rs
  • wavelet_matrix.rs
• io
  • bed.rs
  • fasta.rs
  • fastq.rs
  • gff.rs
  • newick.pest
  • newick.rs
• pattern_matching
  • bndm.rs
  • bom.rs
  • horspool.rs
  • kmp.rs
  • myers
    • builder.rs
    • common_tests.rs
    • helpers.rs
    • long.rs
    • myers_impl.rs
    • simple.rs
    • traceback.rs
  • pssm
    • dnamotif.rs
    • errors.rs
    • protmotif.rs
  • shift_and.rs
  • ukkonen.rs
• scores
  • blosum62.rs
  • pam120.rs
  • pam200.rs
  • pam250.rs
  • pam40.rs
• seq_analysis
  • gc.rs
  • orf.rs
• stats
  • bayesian
    • bayes_factors.rs
    • model.rs
  • combinatorics.rs
  • hmm
    • errors.rs
  • pairhmm
    • homopolypairhmm.rs
    • pairhmm.rs
  • probs
    • adaptive_integration.rs
    • cdf.rs
    • errors.rs
• utils
  • fastexp.rs
  • interval
    • errors.rs
  • text.rs
• types (rust-bio-types)
  • alignment.rs
  • annot
    • contig.rs
    • loc.rs
    • pos.rs
    • refids.rs
    • spliced.rs
  • genome.rs
  • phylogeny.rs
  • sequence.rs
  • strand.rs
  • variant.rs

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Under MIT Licence.