fastasma

A collection of tools for working with FASTA files.

Installation

pip install fastasma

Usage

import fastasma

# Import a FASTA file
source = fastasma.ImportFasta("sequences.fasta")

# Annotate sequences
annotated = fastasma.AddAnnotationToHeader(
    source,
    annotation_key="organism",
    separator="_",
    position="suffix"
)

# Write output
fastasma.WriteFasta(annotated, output_path="output.fasta")

Pipeline example

import fastasma

# Multiple steps can be chained
source = fastasma.ImportFasta("input.fasta")
source = fastasma.DropAnnotationKeys(source, keys_to_remove=["length"])
source = fastasma.AddAnnotationToHeader(source, annotation_key="organism", position="suffix")
source = fastasma.Head(source, n=10)
fastasma.WriteFasta(source, output_path="output.fasta")

Available modules

Importers: ImportFasta, ImportFastas, ImportTSV

Annotators: DropAnnotations, DropAnnotationKeys, AddTaxonomyFromFilename, AddTaxidFromName, AddNameFromTaxid, AddTaxonomicRankFromTaxid, AddAnnotationToHeader

Mutators: Head, Tail, Sample

Writers: WriteFasta, WriteTSV, WriteDB