alignment2hdf5

Simple converter for FASTA and Nexus alignments into HDF5 (Hierarchical Data Format) used in some downstream analyses in ipyrad and other software like superBPP.

This converter has several modes:

1. Convert multiple fasta files in a single folder into a hdf5 file.

Genes or loci must be saved in individual fasta files. They could not include all samples. For example:

gene1.fna

>sample_1
TCTAGACATGCCAGGCGGTGCGTCTGCTGTCGGGTGCCTCTG
>sample_2
TCTAGACATTCCAGGCGGTGCGTCTGCTGTCGGGTGCCTCTA
>sample_3
TCTAGACATTGGAGGCGGTGCGTCTGCTGTCGGGTGCCTCTG

gene2.fna

>sample_1
GTGACTGGCTAGATGGACTTGCCGCTGGTAAAC
>sample_2
GTGACTGGCTAGATGGACTTGCCGCTGGTTTTC

Usage as module:

import alignment2hdf5
alignment2hdf5.multiple_fastas_to_hdf5("./test/genes/*.FNA", output="./test/alignment.hdf5")

Usage as CLI script:

ToDo

2. Split a fasta file into multiple loci having the same length and convert it into a hdf5 file.

Fasta files can be single-lined or multi-lined (interleaved). For example:

simple.fa

>sample_1 single line
TCTAGACATTCCAGGCGGTGCGTCTGCTGTCGGGTGCCTCTG
>sample_2 multiline
TCTAGACATTCCAGGCGGTGC
GTATGCTGTCGGGTGCCTCTG

Usage as module:

import alignment2hdf5
alignment2hdf5.split_fasta_to_hdf5("./test/fasta.fa", number_loci=4, output="./test/fasta.hdf5")

Usage as CLI script:

ToDo

3. Convert nexus file into a hdf5 file.

Nexus file can be sequential or interleaved. File must have charpartition block in order to split every locus in the main matrix. This script also can parse taxpartition block to create an imap file.

simple.nex

 #NEXUS
[This is an example of nexus file]

Begin data;
    Dimensions ntax=6 nchar=48;
    Format datatype=nucleotide gap=- missing=?;
    Matrix
a1    CTGATTTACATGTCAGATGTTTTTACTAGTTCCCAACAGTTTCTCATG
a2    CTGATTTACATGTCAGATGTTTTTACTAGTTCCCAACAGTTTCTCATG
b1    CTGATTTACATGTCAGATGTTTTTACTAGTTCCCAACAGTTTCTCATG
b2    CTGATTTACATGTCAGATGTTTTTACTAGTTCCCAACAGTTTCTCATG
c1    CTGATTTACATGTCAGATGTTTTTACTAGTTCCCAACAGTTTCTCATG
c2    CTGATTTACATGTCAGATGTTTTTACTAGTTCCCAACAGTTTCTCATG
    ;
End;

[charpartition block is requiered]
charpartition lociset =
1: 1-10,
2: 11-20,
3: 21-30,
4: 31-40,
5: 41-48;
end;

Usage as module:

import alignment2hdf5
alignment2hdf5.nexus_to_hdf5("./test/nexus.nex", output="./test/nexus.hdf5")

Usage as CLI script:

ToDo