alias-mapper 1.0.0

Translate chromosome/scaffold names in bioinformatics files between naming conventions

alias-mapper

Translate chromosome and scaffold names in bioinformatics files between naming conventions (GenBank, RefSeq, UCSC, and others).

What it does

Research files from different sources use different names for the same sequences: chr1, NC_000001.11, CM000663.2, and 1 can all refer to the same human chromosome. Files using different conventions can't be combined without translation.

alias-mapper rewrites the sequence names in GFF, GTF, and FASTA files from one convention to another using a precomputed alias table built from NCBI assembly reports. Source convention and genome assembly are auto-detected from the input by default.

Install

pip install git+https://github.com/guigolab/alias-mapper.git

On networks that perform TLS inspection (corporate / institutional, e.g. CRG), also install the trusted extra so the tool uses the system keychain for cert verification:

pip install "alias-mapper[trusted] @ git+https://github.com/guigolab/alias-mapper.git"

The first time you run convert, the tool downloads the latest alias data (~100 MB) from GitHub Releases and builds a local SQLite database in your platform cache directory:

• macOS: ~/Library/Caches/alias-mapper/aliases.db
• Linux: ~/.cache/alias-mapper/aliases.db
• Windows: %LOCALAPPDATA%\alias-mapper\Cache\aliases.db

First-run setup takes about a minute. Subsequent runs use the cached database directly. If the database schema changes in a newer release, the cache is rebuilt automatically.

Quickstart

alias-mapper convert annotations.gff --to ucsc -o annotations.ucsc.gff

A summary on stderr reports how many rows were translated and how many had sequence names not in the alias database (those rows are passed through unchanged with a warning).

Usage

# single file
alias-mapper convert <input> --to <convention> -o <output> [options]

# multi-file: conform annotations to a reference FASTA (FASTA untouched)
alias-mapper convert --fasta <ref> [<ann> ...] --out-dir <dir> [options]

# multi-file: force the FASTA and annotations to one convention
alias-mapper convert --fasta <ref> [<ann> ...] --overwrite-to <convention> --out-dir <dir>

alias-mapper update

Subcommands

• convert — translate a single file, or a reference FASTA plus its annotation files (multi-file mode; see Multi-file mode).
• update — re-download the latest alias data and rebuild the cached database. Run manually when you want newer data.

Supported file types

GFF (.gff, .gff3), GTF (.gtf), and FASTA (.fa, .fasta, .fna). The translator is picked by file extension.

Supported conventions

genbank, refseq, ucsc, sequence-name, assigned-molecule.

Examples

# Translate from RefSeq to UCSC explicitly
alias-mapper convert annotations.gff \
    --from refseq --to ucsc \
    -o out.gff

# Pin the assembly when auto-detection is ambiguous
alias-mapper convert annotations.gff \
    --to ucsc \
    --assembly GCF_000001405.40 \
    -o out.gff

# FASTA — same syntax, different file
alias-mapper convert reference.fa \
    --from genbank --to sequence-name \
    --assembly GCA_963924405.1 \
    -o reference.renamed.fa

# Multi-file conform: rewrite the annotations to match reference.fa's
# own convention; reference.fa is left untouched
alias-mapper convert --fasta reference.fa genes.gff peaks.bed.gff \
    --out-dir conformed/

# Multi-file overwrite: force reference.fa and its annotations to UCSC
alias-mapper convert --fasta reference.fa genes.gff \
    --overwrite-to ucsc --out-dir ucsc_out/

# Refresh the cached alias data
alias-mapper update

Multi-file mode

Pass --fasta <ref> to process a reference FASTA together with its annotation files in one invocation. The assembly is detected once from the FASTA and the alias table is loaded once for the whole batch. Outputs go to --out-dir, named <stem>.<convention>.<ext> (gzip preserved).

There are two modes:

• Conform (the default, when --overwrite-to is omitted): each annotation is rewritten to match the FASTA's own convention, and the FASTA is left unchanged. Use this to make a set of annotations agree with a genome you already have. The FASTA is not copied into the output directory, since it is unchanged.
• Overwrite (--overwrite-to <convention>): the FASTA and every annotation are converted to the named convention.

--to is single-file only; in --fasta mode use --overwrite-to (or omit it to conform).

Flags (convert)

Flag	Mode	Purpose
--to	single-file	Target naming convention (required in single-file mode)
-o	single-file	Output path
--fasta	multi-file	Reference FASTA; enables multi-file mode
--overwrite-to	multi-file	Force the FASTA and all annotations to this convention
--out-dir	multi-file	Output directory for the converted files
--from	both	Source convention. Auto-detected if absent (not used to conform)
--assembly	both	Assembly accession. Auto-detected if absent
--alias-db	both	Path to a specific alias SQLite database (overrides cache)

Auto-detection

When --from or --assembly is omitted, the tool reads up to 50 unique sequence names from the input and scores them against the database. It commits to a result only when the top candidate has at least 5 matches and beats the runner-up by 2× or more. Otherwise it errors out and asks for the flag explicitly.

Unmapped names

If a sequence name in the input isn't in the alias database, the line is written to the output unchanged and counted in the unmapped total. Up to five example names are printed at the end of the run so you can see what didn't translate.

Before giving up on a name, the tool tries a couple of conservative fallbacks: swapping a UCSC-style vN version separator for the .N form (and vice versa), and stripping an ENA|...|accession header wrapper down to the bare accession. These only run when the exact name isn't found, so they never override a direct match.

Data updates

A weekly GitHub Actions workflow rebuilds the alias dataset from NCBI's published assembly summaries and publishes it as a data-YYYY-MM-DD GitHub Release. Each release ships three artifacts:

• aliases.tsv.gz — the merged-row alias data the CLI consumes.
• historical.tsv.gz — dead-accession lookup with suppression dates and best-effort replacements.
• failures.tsv — per-assembly collection failure log.

More

See docs/design.md for architecture, design decisions, and direction.