NucleicTools

Tools for working with nucleotides and their sequences.

Modules

DNA/RNA Tools

The aggregation function run_dna_rna_tools processes DNA or RNA sequences with various operations.

The aggregation function run_dna_rna_tools accepts an arbitrary number of arguments containing DNA or RNA sequences (str), as well as the name of the procedure to be executed (this is always the last argument; see the usage example), performs the specified operation on all the passed sequences and returns the result.

The following procedres are available:

is_nucleic_acid - returns a Boolean result of a sequence check

is_rna - returns a Boolean result of a RNA-sequence check

is_dna - returns a Boolean result of a DNA-sequence check

transcribe - returns the transcribed sequence

reverse - returns the reversed sequence

complement - returns the complementary sequence

reverse_complement - returns the reverse complementary sequence

run_dna_rna_tools usage example

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']

FASTQ Filtering

The filtration function filter_fastq accepts four arguments (seqs, gc_bounds, length_bounds, quality_threshold) and returns a dictionary similar to the input one, but consisting only of those sequences that satisfy all filtering conditions.

seqs is a dictionary of fastq sequences: key is a string name of the sequence, the value is a tuple of two strings: the sequence and the quality in phred33 scale.

gc_bounds - the GC-content interval (in percent), by default is (0, 100). If a single number is passed as an argument, it is considered to be the upper limit.

length_bounds - the length interval, by default is (0, 2**32).

quality_threshold - the average read quality threshold for filtering; by default, it is 0 (phred33 scale).

filter_fastq usage example

fastq_dict = {
    "read_1": ("ATCGATCGAT", "IIIIIIIIII"),
    "read_2": ("GGCCGGCCGG", "=;@B??@<>@"),
    "read_3": ("TTTTAAAAAA", "HHHHHHHHHH"),
    "read_4": ("ACGTACGTAC", "FFFFFFFFF#"),
    "read_5": ("GGGGGGGGGG", "GFFCFEEEFF"),
    "read_6": ("ATATATATAT", "EEEEEEEEEE"),
    "read_7": ("CGCGCGCGCG", "GGGGGGGGGG"),
    "read_8": ("AAAAAAAAAA", "DDDDDDDDDD"),
    "read_9": ("TAGCTAGCGA", "IIIIIIIIII"),
    "read_10": ("CCCCCCCCCC", "D@EDEFFB=D")
}

filter_fastq(fastq_dict, 100, 9, 37)

bio_files_processor

convert_multiline_fasta_to_oneline:

reads a fasta file supplied as input,
in which the sequence (DNA/RNA/protein/etc.) can be split into several lines,
and then saves it into a new fasta file in which each sequence fits one line.

select_genes_from_gbk_to_fasta:

function receives a GBK-file as input, 
extracts the specified number of genes before and after each gene of interest (gene), 
and saves their protein sequence (translation) to a fasta file.

Error Handling

Functions raise appropriate exceptions for invalid inputs.

Requirements:

Python 3.11+

License

MIT License - see LICENSE file for details.