Python - microbiorust-py

For ease of use you can call directly from Python

No need to install Rust

Install microbiorust-py using pip:

pip install microbiorust

example script for converting from GenBank to protein fasta:

from microbiorust import gbk_to_faa
result = gbk_to_faa("filename.gbk") 
for r in result:
   print(r)

microbiorust-py contains the following features:

GenBank input:

gbk_to_faa # converts gbk format to protein fasta
gbk_to_fna # converts gbk format to DNA sequence contigs fasta
gbk_to_ffn # converts gbk format to DNA gene sequence fasta
gbk_to_gff # converts gbk format to GFF3
gbk_to_faa_count # counts numbers of protein fasta converted from gbk

EMBL input:

embl_to_faa
embl_to_fna
embl_to_gff

BLAST input:

parse_tabular # streaming parse BLAST input as -outfmt 6
parse_XML # streaming BLAST parser for -outfmt 5

Alignment input (MSA):

subset_msa_alignment # subset the alignment by row and column
get_consensus # get a consensus sequence for your MSA alignment

Calculate sequence metrics:

hydrophobicity
amino_counts # counts of each amino acid in the provided sequence
amino_percentage # percentage of each amino acid in the provided sequence