SynMap_helper_scripts

Tools to facilitate Synteny analysis using SynMap

Inversion of nucleotide FASTA and GFF files

invert_fasta.py & invert_gff.py

• invert_fasta.py: This script inverts nucleotide sequences in a multi-contig FASTA file by generating their reverse complement.
• invert_gff.py: This script prepares a GFF file with inverted coordinates. It requires an input GFF3 file along with the associated nucleotide FASTA file to correctly compute the inverted positions and strands.

Output

• invert_fasta.py: Outputs a new FASTA file with reverse-complemented sequences.
• invert_gff.py: Outputs a new GFF3 file with inverted coordinates and strand information.

Note

You can use the agat_convert_sp_gxf2gxf.pl command from agat package to modify the generated inverted gff files for SynMap compatibility:

Use

agat_convert_sp_gxf2gxf.pl --gff inverted_gff -o Synmap_compatible_inverted_gff

get_CDS_AA.py

This script extract cds based on an input of GFF3 and corresponding nucelotide FASTA file, then translate the cds to amino acids (AA).

Output

-Nucelotide FASTA file representing identified cds.

-AA FASTA file representing the translated cds.

The scripts rely on Biopython for functionality.

Installation

with conda:

conda install -c conda-forge biopython