fastasma

A collection of tools for working with FASTA files.

Installation

pip install fastasma

Usage

Pipeline example

import fastasma

source = fastasma.ImportFasta("input.fasta")
source = fastasma.DropAnnotationKeys(source, keys_to_remove=["length"])
source = fastasma.AddAnnotationToHeader(source, annotation_key="organism", position="suffix")
source = fastasma.FilterByLen(source, is_="greater", length=200)
source = fastasma.DeduplicateHeaders(source, separator="_")
source = fastasma.Head(source, n=10)
fastasma.WriteFasta(source, output_path="output.fasta")

Modules

Importers

Read sequences from files or directories.

Class	Description
`ImportFasta(filepath)`	Reads a single FASTA file. Parses header annotations in `[key=value]` format.
`ImportFastas(filepaths=None, directory=None)`	Reads multiple FASTA files from a list or directory.
`ImportTSV(filepath, header_idx=0, seq_idx=1, annotation_idx=None, header=True)`	Reads sequences from a TSV file with configurable column indices.

Annotators

Modify sequence annotations or headers.

Class	Description
`DropAnnotations(source)`	Removes all annotations from every sequence.
`DropAnnotationKeys(source, keys_to_remove)`	Removes specific annotation keys by name.
`AddTaxonomyFromFilename(source, key, header_formatter=None)`	Extracts a taxon from the source filename and adds it to the header.
`AddTaxidFromName(source, taxonomy_db, organism_field="organism")`	Looks up organism names in a SQLite taxonomy DB and adds the corresponding `taxid`.
`AddNameFromTaxid(source, taxonomy_db, taxid_field="taxid", name_field="organism")`	Converts taxid values to scientific names using a taxonomy DB.
`AddTaxonomicRankFromTaxid(source, taxonomy_db, taxid_field="taxid", rank="species")`	Traverses NCBI taxonomy tree to find a given rank (e.g., `"order"`) for each taxid.
`AddAnnotationToHeader(source, annotation_key, separator="_", position="suffix")`	Adds an annotation value as prefix or suffix to the sequence header.

Mutators

Filter, sample, rename, or transform the sequence stream.

Class	Description
`Head(source, n)`	Yields the first `n` sequences.
`Tail(source, n)`	Yields the last `n` sequences.
`Sample(source, k, seed=None)`	Randomly samples `k` sequences using reservoir sampling.
`DeduplicateHeaders(source, separator="_", position="suffix", start=1)`	Renames duplicate headers by appending a counter (e.g., `seq01`, `seq01_1`, `seq01_2`).
`FilterByLen(source, is_, length)`	Filters sequences by length. `is_` can be `"greater"`, `"greater_equal"`, `"less"`, `"less_equal"`, or `"equal"`.

Writers

Write sequences to output files or databases.

Class	Description
`WriteFasta(source, output_path, wrap=80)`	Writes sequences to a FASTA file with configurable line wrapping.
`WriteTSV(source, output_path, sep="\t")`	Writes sequences to a TSV file with annotations as columns.
`WriteDB(source, db_path)`	Writes sequences to a SQLite database with normalized annotation tables.

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

fastasma-0.1.5.tar.gz (10.4 kB view details)

Uploaded Jul 22, 2026 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

fastasma-0.1.5-py3-none-any.whl (11.2 kB view details)

Uploaded Jul 22, 2026 Python 3

File details

Details for the file fastasma-0.1.5.tar.gz.

File metadata

Download URL: fastasma-0.1.5.tar.gz
Upload date: Jul 22, 2026
Size: 10.4 kB
Tags: Source
Uploaded using Trusted Publishing? No
Uploaded via: twine/6.2.0 CPython/3.13.11

File hashes

Hashes for fastasma-0.1.5.tar.gz
Algorithm	Hash digest
SHA256	`fbe42c9985bcd6741b9d3610a0ecf4b89ffd58d41bf177a0ade4725f18490905`
MD5	`a907ea7dd6c14bdd3531d069fadf352d`
BLAKE2b-256	`e712e8652c3379b0471a62a20735f51841f4dd8815dafa037c6369b9d7c126f0`

See more details on using hashes here.

File details

Details for the file fastasma-0.1.5-py3-none-any.whl.

File metadata

Download URL: fastasma-0.1.5-py3-none-any.whl
Upload date: Jul 22, 2026
Size: 11.2 kB
Tags: Python 3
Uploaded using Trusted Publishing? No
Uploaded via: twine/6.2.0 CPython/3.13.11

File hashes

Hashes for fastasma-0.1.5-py3-none-any.whl
Algorithm	Hash digest
SHA256	`7d75acbd40ee2daae95648dbf58ff32bcd2edc4947d6c6fc136b0627b9953baa`
MD5	`fe4358919f600dab3db6245b59ec9b1e`
BLAKE2b-256	`2f87cd6ce5432247728abce36dcd2fd4c66bfe93df1bc2b61525826c9ac7e6a4`