These Python programs characterize sequences in a fasta file, including telomere information.
ACKNOWLEDGEMENT
This code was written by David Winter. It is posted here to allow for automated git cloning.
INSTALLATION
summarize_contigs requires the biopython package. This can be installed with
pip install biopython
CODE VARIANTS
summarize_contigs looks for the typical fungal telomere sequence TAACCC. summarize_contigs_phytophthora looks for the typical Phytophthora telomere sequence TAAACCC.
USAGE
Program usage is as follows:
summarize_contigs.py FASTA_input_file > summary_file.tsv
summarize_contigs_phytophthora.py FASTA_input_file > summary_file.tsv
EXAMPLE
summarize_contigs.py fungal_assembly.fna > assembly_summary.tsv
summarize_contigs_phytophthora.py phytophthora_assembly.fna > assembly_summary.tsv