BioGen is a toolkit for genetic data processing. It allows you to evaluate, validate, and prepare your nucleotide sequences for downstream analysis, including FASTQ filtering by GC%, length, and quality; FASTA reformatting; BLAST best-hit extraction; and retrieval of flanking genes from GenBank files.
Authors:
- Andrey Nekrasov
- Gregor Mendel
- James D. Watson
- Francis H.C. Crick
BioGen documentation is available at https://site.lol/this/link/does/not/exists
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run_dna_rna_tools - Performs validation and various operations on a nucleotide sequence (DNA or RNA).
run_dna_rna_tools('TTUU', 'is_nucleic_acid') # False !!
run_dna_rna_tools('ATG', 'transcribe') # 'AUG'
run_dna_rna_tools('ATG', 'reverse') # 'GTA'
run_dna_rna_tools('AtG', 'complement') # 'TaC'
run_dna_rna_tools('ATg', 'reverse_complement') # 'cAT'
run_dna_rna_tools('ATG', 'aT', 'reverse') # ['GTA', 'Ta']filter_fastq - Filter FASTQ reads by GC%, length, and mean Phred quality; write passing reads to output.
filter_fastq(seqs = EXAMPLE_FASTQ, gc_bounds = (20, 80), length_bounds = (10, 30), quality_threshold = 10)convert_multiline_fasta_to_oneline – Converts multi-line FASTA sequences into a single-line format and saves the result.
convert_multiline_fasta_to_oneline(input_fasta: "input.fasta", output_fasta: "output.fasta")parse_blast_output - Parses a BLAST output file and keeps only the best match for each query sequence.
parse_blast_output(input_file: "input.txt", output_file: "output.txt")select_genes_from_gbk_to_fasta - Extracts the nearest flanking genes of a target gene from a GenBank file and saves them in FASTA format.
select_genes_from_gbk_to_fasta(input_gbk: "input.gbk", genes: ["gene1", "gene2"], n_before: 20, n_after: 25, output_fasta: "output.fasta")The MIT License (Made In Tears)