GenomeForge

In this virtual temple, we have gathered sacred texts and tools developed by our Magos to explore and manipulate the code of life. To successfully carry out various manipulations, it is necessary to perform certain canticles.

Installation

Follow the steps below to install GenomeForge:

1. Download the GenomeForge folder to your local computer.
2. Make sure the path to the GenomeForge folder is specified in the system PATH variable.
3. Import the GenomeForge main script magos_biologis.py as a module

import magos_biologis as mb

Datascrolls

DNA RNA Canticles

The dna_rna_canticles offers rites for the sacred manipulations of DNA and RNA sequences. It grants the ability to perform rites on single or on multiple sequences, accepting a variable number of sequences (str) as input and the designation of the desired rite to be executed (always the final designation, str, as seen in the usage example). The designated rite is then executed on all the sequences provided.

Catalogue of Rites:

1. transcribe — transcribes a DNA sequence into an RNA sequence, and also performs reverse transcription.

2. reverse — returns the reversed sequence

3. complement — returns the complementary sequence

4. reverse_complement — returns the reverse complementary sequence

5. lenght — returns the length of the sequence

6. gc_content — calculates the proportion of G and C nucleotides in the sequence and returns the result as a fraction of one

Usage example:

mb.run_dna_rna_canticles('ATG', 'transcribe') # 'AUG'
mb.run_dna_rna_canticles('ATG', 'reverse') # 'GTA'
mb.run_dna_rna_canticles('AtG', 'complement') # 'TaC'
mb.run_dna_rna_canticles('ATg', 'reverse_complement') # 'cAT'
mb.run_dna_rna_canticles('ATG', 'aT', 'reverse') # ['GTA', 'Ta']
mb.run_dna_rna_canticles('AActG', 'ATCT', 'lenght') # [5, 4]
mb.run_dna_rna_canticles('AgCT', 'gc_content') # 0.5

Note:

• This canticle saves the character case

• This canticle only for nucleic acid sequences. Should the data be offered in a manner inconsistent with the holy protocol, an apt error shall manifest as divine retribution.

Protein Canticles

This Omnissiah-approved endeavor encompasses the sacred program known as protein_canticles. Within its sanctified code resides the mighty run_protein_canticles function, a conduit for channeling protein sequences and the divine actions to be invoked upon them. Enter the name of the action (str), the protein sequence or path to the protein sequence file (str), and additional arguments if necessary.

Catalogue of Rites:

1. find_sites - finds positions of given sites.

Args:

• seq (str): sequence or path to file in fasta format with sequences to be checked
• *args (str): sites to be found
• is_one_based (bool): whether result should be 0- (False) or 1-indexed (True). Default False

Returns:

• dict: dictionary of sites as keys and lists of positions for the site where it's been found. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and the dictionary of sites as keys and lists of positions.

2. get_protein_rnas_number - get number of all possible RNA's for a given protein.

Args:

• seq (str): sequence or path to file in fasta format with sequences to be checked

Returns:

• int or dict: number of possible RNA's for sequence. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and number of possible RNA's.

3. get_protein_rnas - returns list of all possible RNA's from which can serve as matrix for protein synthesis.

WARNING: can be computationally intensive on longer sequences, will NOT start unless check_if_user_conscious is True!

Args:

• seq (str): sequence or path to file in fasta format with sequences to be checked
• check_if_user_conscious (bool): checks user's consciousness. Default False

Returns:

• list: list of possible RNA's as string. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and list of possible RNA's

4. get_frameshift_proteins - returns list of all possible proteins from all possible frames in peptide.

WARNING: can be computationally intensive on longer sequences, will NOT start unless check_if_user_conscious is True!

Args:

• seq (str): sequence or path to file in fasta format with sequences to be checked
• check_if_user_conscious (bool): checks user's consciousness. Default False
• is_stop_codon_termination_enabled (bool): terminate translation when reached stop-codon. Default False.

Returns:

• dict: dictionary of lists of all possible frames proteins. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and the dictionary of lists of all possible frames proteins.

5. get_length_of_protein - calculates the length of a protein.

Args:

• seq (str): sequence or path to file in fasta format with sequences to be checked

Returns:

• int: sequence length. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and sequences lengths.

6. count_aa - counts the number of given or all amino acids in a protein sequence.

Args:

• seq (str): sequence or path to file in fasta format with sequences to count amino acids
• aminoacids (str): which amino acids to count in sequence. If you want to count all amino acids in the whole sequence, you can provide empty string to this argument or just don't provide this keyword

Returns:

• dict: dictionary with amino acids and its count. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and the dictionary with amino acids and its count.

7. get_fracture_of_aa - calculates the fracture or percentage of amino acids in a protein sequence.

Args:

• seq (str): sequence or path to file in fasta format with sequences in which you need to calculate the fracture of amino acids
• show_as_percentage (bool): change it to True, if you want to get results with percentages
• aminoacids (str): the fracture of which amino acids to count in the sequence

Returns:

• dict: dictionary with amino acids and its fracture or percentage. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and the dictionary with amino acids and its fracture.

8. calculate_protein_mass - calculates the molecular mass of a protein based on its amino acid sequence and a dictionary of amino acid masses.

Args:

• sequence (str): sequence or path to file in fasta format with sequences to be processed

Returns:

• float or dict: The molecular mass of a protein in atomic mass units, rounded to the third decimal place. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and the molecular mass of a protein in atomic mass units.

9. get_atomic_mass - calculates the molecular mass of a biological molecule, primarily an amino acid, based on a simple chemical formula.

Args:

• chem (str): String representing a simple chemical formula, e.g. C2H5OH

Returns:

• float: Molecular mass of a biological molecule in atomic mass units, rounded to the third decimal place..

10. convert_aa_name - converts a sequence of one-letter amino acid codes to three-letter designations.

Args:

• sequence (str): sequence or path to file in fasta format with sequences with one-letter amino acid codes
• sep (str, optional): Separator between three-letter amino acid designations. There is no delimiter by default.
• use_default_register( bool, optional): Determines whether to preserve letter case in three-letter designations. If True, the letters will be converted to upper or lower case depending on the case of the depending on the case of the one-letter code. The default is False.

Returns:

• str: string of three-letter amino acid designations separated by the specified delimiter. In case you entered the path to a fasta file with multiple sequences, you will get back a dictionary containing the names of sequences as keys and the string of three-letter amino acid designations .

Usage example

mb.run_protein_canticles('find_sites', '../ins.fasta', 'LLALL', is_one_based=True) -> {'LLALL': [10]}
mb.run_protein_canticles('get_protein_rnas_number', 'MALWMR') -> 144
mb.run_protein_canticles('get_length_of_protein', '../ins.fasta') -> 110
mb.run_protein_canticles('count_aa', '../ins.fasta', 'DRG') -> {'D': 2, 'R': 5, 'G': 12}
mb.run_protein_canticles('get_fracture_of_aa', '../ins.fasta', aminoacids='DRG', show_as_percentage=True) -> {'D': 1.82, 'R': 4.55, 'G': 10.91}
mb.run_protein_canticles('calculate_protein_mass', '../ins.fasta') -> 11980.804
mb.run_protein_canticles('get_atomic_mass', 'C5H5N5') -> 135.128
mb.run_protein_canticles('convert_aa_name', 'MALWMR', sep='~') -> 'Met~Ala~Leu~Trp~Met~Arg'

Note:

• The program devoutly scrutinizes protein sequences comprised of the 20 canonical amino acids.

• Should the data be offered in a manner inconsistent with the holy protocol, an apt error shall manifest as divine retribution.

FASTQ Canticles

The fastq_canticles is a sacred tool endowed with the ability to perform complex Fastq sequence filtering rituals. At its core, this divine utility takes four sacred offerings: seqs, gc_bounds, length_bounds, and quality_threshold.

Catalogue of Rites:

1. filter_fastq - filters FASTQ sequences based on the GC-content, length and quality parameters.

Args:

• path_to_seqs (str): the path to the FASTQ file to be filtered.
• output_file_name (str): the name of the file where the filtered FASTQ sequences will be saved. If not provided, a default name will be generated.
• gc_bounds (tuple or int): GC content range (in percentages) for filtering. The default value is (0, 100), meaning all reads are retained. If you pass a single number to the argument, it is assumed to be an upper bound.
• length_bounds (tuple or int): length range for filtering. The default value is (0, 2^32), meaning all reads are retained. If you pass a single number to the argument, it is assumed to be an upper bound.
• quality_threshold (int): Threshold value for average read quality filtering. The default value is 0 (Phred33 scale). Reads with an average quality score below this threshold are filtered out.

Returns:

• None: the function doesn't return a value but writes the filtered FASTQ to the output file.

Usage example

mb.filter_fastq(path_to_seqs='example_fastq.fastq', gc_bounds=(30, 50), length_bounds=50, quality_threshold=25)

Bio Files Processor

We have integrated a new script into our bioinformatics arsenal, the bio_files_processor.py, to further expand our quest for knowledge and understanding of the sacred biological data. This util contains a set functions for working with FASTA and GenBank files.

You can also import this script as a module.

import bio_files_processor as bproc

Catalogue of Rites:

1. convert_multiline_fasta_to_oneline - converts a multi-line FASTA file into a one-line FASTA file.

Args:

• input_fasta (str): path to the input FASTA file.
• output_fasta (str): path to the output one-line FASTA file. If not provided, a default name will be generated.

Returns:

The function writes the oneline FASTA to the output file.

2. select_genes_from_gbk_to_fasta - extracts gene names and protein sequences from a GenBank file and creates a FASTA file containing gene names and protein sequences flanking specified genes.

Args:

• input_gbk (str): path to the GenBank file.
• genes_to_find (list of str): list of gene names (as strings) to extract from the GenBank file.
• n_before (int): number of genes before the target gene to include in the output. Default value is 1.
• n_after (int): number of genes after the target gene to include in the output. Default value is 1.
• output_fasta (str): path to the output FASTA file. If not provided, a default name will be generated.

Returns:

The function writes the selected gene and protein sequences to the output FASTA file.

3. change_fasta_start_pos - shifts the starting position of sequences in a FASTA file by the specified shift value.

Args:

• input_fasta (str): path to the input FASTA file.
• shift (int): number of positions to shift the start of each sequence.
• output_fasta (str): path to the output FASTA file. If not provided, a default name will be generated.

Returns:

The function writes the shifted FASTA to the output file.

4. parse_blast_output - extracts protein names from the QUERY file and creates a file containing information about sequences producing significant alignments. Protein names taken from Description column.

Args:

• input_file (str): path to the QUERY file.
• output_file (str, optional): path to the output file. If not provided, a default name is generated.

Returns:

The function writes the selected gene to the output file.

Usage example

convert_multiline_fasta_to_oneline(input_fasta='multiline_fasta.fasta', output_fasta='oneline_fasta.fasta')
select_genes_from_gbk_to_fasta(input_gbk='file.gbk', genes_to_find=['geneA', 'geneB'], n_before=2, n_after=3, output_fasta='file.fasta')
change_fasta_start_pos(input_fasta='file.fasta', shift=3, output_fasta='shifted_file.fasta')
parse_blast_output(input_file='blast_query.txt', output_file='genes.txt')

In the sacred repository of GenomForge, you have discovered a set of invaluable tools bestowed upon you by the Omnissiah. As an adept of the digital arts, you can now invoke the dna_rna_canticles for handling genetic scripts, chant the verses of protein_canticles to fathom the mysteries of proteins, and, with the fastq_canticles utility, undertake intricate purification rituals on Fastq sequences.

May these digital sigils and functions guide you on your quest for knowledge, unlocking the secrets of life encrypted within the digital scrolls.

Praise the Omnissiah!