reform

reform is a python-based command line tool that allows for fast, easy and robust editing of reference genome sequence and annotation files.

Execution of reform requires a reference sequence (fasta), reference annotation (GFF or GTF), the novel sequences to be added (fasta), and corresponding novel annotations (GFF or GTF). A user provides as arguments the name of the modified chromosome and either the position at which the novel sequence is inserted, or the upstream and downstream sequences flanking the novel sequences. This results in the addition and/or deletion of sequence from the reference in the modified fasta file. In addition to the novel annotations, any changes to the reference annotations that result from deleted or interrupted sequence are incorporated into the modified gff. Importantly, modified gff and fasta files include a record of the modifications.

Learn more at https://gencore.bio.nyu.edu/reform/

Usage

reform requires Python3, pgzip and Biopython v1.78 or higher.

Install pgzip and biopython if you don't already have it:

pip install pgzip
pip install biopython

Invoke the python script:

python3 reform.py 
  --chrom=<chrom> \
  --position=<pos> \ 
  --in_fasta=<in_fasta> \
  --in_gff=<in_gff> \
  --ref_fasta=<ref_fasta> \
  --ref_gff=<ref_gff>

Parameters

chrom ID of the chromsome to modify

position Position in chromosome at which to insert <in_fasta>. Can use -1 to add to end of chromosome. Note: Either position, or upstream AND downstream sequence must be provided. Note: Position is 0-based

upstream_fasta Path to Fasta file with upstream sequence. Note: Either position, or upstream AND downstream sequence must be provided.

downstream_fasta Path to Fasta file with downstream sequence. Note: Either position, or upstream AND downstream sequence must be provided.

in_fasta Path to new sequence to be inserted into reference genome in fasta format.

in_gff Path to GFF file describing new fasta sequence to be inserted.

ref_fasta Path to reference fasta file.

ref_gff Path to reference gff file.

Example

python3 reform.py 
  --chrom="I" \
  --upstream_fasta="data/up.fa" \
  --downstream_fasta="data/down.fa" \
  --in_fasta="data/new.fa" \
  --in_gff="data/new.gff" \
  --ref_fasta="data/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa" \
  --ref_gff="data/Saccharomyces_cerevisiae.R64-1-1.34.gff3"

Output

reformed.fa Modified fasta file.

reformed.gff3 Modified GFF file.