reform is a Python-based command-line tool for fast, robust, and flexible editing of reference genome sequence and annotation files.
To perform an edit, reform requires a reference genome (FASTA), its annotation file (GFF or GTF), a novel sequence to be inserted (FASTA), and the corresponding annotation (GFF or GTF). The user specifies either:
- the chromosome and the position at which to insert the novel sequence, or
- the chromosome along with the upstream and downstream flanking sequences.
The result is a modified reference genome (FASTA) and annotation file (GFF), incorporating the novel sequence and its annotations. Any reference annotations affected by the insertion or deletion are automatically updated. All modifications are documented within the output files.
In addition to modifying existing chromosomes, reform also supports appending entirely new chromosomes. In this mode, users provide the novel chromosome’s sequence and annotations, which are added to the reference genome and integrated into the annotation file.
Learn more at https://gencore.bio.nyu.edu/reform/
reform requires Python3 and Biopython v1.78 or higher.
Install biopython if you don't already have it:
pip install biopython>=1.78
reform supports reading and writing .gz files using gzip. To accelerate compression and decompression, it optionally supports pgzip, a parallel implementation of gzip. Users must install pgzip separately to enable this feature.
Optional: Install pgzip if you don't already have it:
pip install pgzip
Invoke the python script:
### Minimal Example (Single Edit)
python3 reform.py \
--chrom=<chrom> \
--position=<position> \
--in_fasta=<input_fasta.fa> \
--in_gff=<input_annotations.gff> \
--ref_fasta=<reference_genome.fa> \
--ref_gff=<reference_annotations.gff3>
-
chrom: ID of the chromosome to modify. Required unlessnew_chromis specified. Cannot be used together withnew_chrom. -
new_chrom: ID of the novel chromosome to append. Required if you're adding a new chromosome. Cannot be used together withchrom. -
position: 0-based insertion position(s) in the reference chromosome wherein_fastashould be inserted. Use-1to insert at the end of the chromosome. For multiple edits, provide a comma-separated list (e.g.,0,5,-1). Note: Eitherposition, or bothupstream_fastaanddownstream_fasta, must be provided. -
upstream_fasta: Path(s) to FASTA file(s) containing the upstream flanking sequence(s) for insertion. For multiple edits, provide a comma-separated list (e.g.,up1.fa,up2.fa,up3.fa). Must be used withdownstream_fasta. Cannot be used together withposition. -
downstream_fasta: Path(s) to FASTA file(s) containing the downstream flanking sequence(s) for insertion. For multiple edits, provide a comma-separated list (e.g.,down1.fa,down2.fa,down3.fa). Must be used withupstream_fasta. Cannot be used together withposition. -
in_fasta: Path(s) to FASTA file(s) containing the new sequence(s) to insert. For multiple edits, provide a comma-separated list. The number of entries must match the number ofpositionvalues or the number of upstream/downstream pairs. -
in_gff: Path(s) to GFF3 file(s) describing thein_fastasequence(s). For multiple edits, provide a comma-separated list. The number of entries must match the number ofin_fastafiles. -
ref_fastaPath to the reference genome FASTA file. -
ref_gffPath to the reference genome annotation (GFF3 or GTF) file.
python3 reform.py \
--chrom="I" \
--position=1500 \
--in_fasta="data/edit.fa" \
--in_gff="data/edit.gff" \
--ref_fasta="data/ref.fa" \
--ref_gff="data/ref.gff3"
python3 reform.py \
--chrom="I" \
--upstream_fasta="data/up.fa" \
--downstream_fasta="data/down.fa" \
--in_fasta="data/edit.fa" \
--in_gff="data/edit.gff" \
--ref_fasta="data/ref.fa" \
--ref_gff="data/ref.gff3"
python3 reform.py \
--chrom="I" \
--position=1000,2500,3000 \
--in_fasta="data/edit1.fa,data/edit2.fa,data/edit3.fa" \
--in_gff="data/edit1.gff,data/edit2.gff,data/edit3.gff" \
--ref_fasta="data/ref.fa" \
--ref_gff="data/ref.gff3"
python3 reform.py \
--new_chrom="new_chr1" \
--in_fasta="data/new1.fa" \
--in_gff="data/new1.gff" \
--ref_fasta="data/ref.fa" \
--ref_gff="data/ref.gff3"
reformed.fa Modified fasta file.
reformed.gff3 Modified GFF file.
After local deployment or modification, you can run test_reform.py to verify the functionality of reform. This script contains an automated test suite built with Python’s unittest framework and validates reform across a range of genome editing scenarios.
To run all tests:
python3 test_reform.py