SequenceMaster

P.S. You may run test.py in terminal/command line to check the code! Hope you enjoy it!

A powerful and minimalistic bioinfomatical tool to work with sequences of nucleic acids and proteins. Moreover, you may manipulate with your data in FASTQ, FASTA and GBK formats

Key Features

Nucleic Acid Analysis: SequenceMaster offers comprehensive tools for analyzing DNA and RNA sequences.
Protein Analysis: Explore protein sequences with advanced tools for pI calculation, protein mass calculation,
FASTQ File Filtering: Easily filter FASTQ files depending on quality, sequence length and GC content
FASTA File Manipulation: Convert multiline FASTA to oneline FASTA and shift starting point
GBK Data Extraction: Extract sequence of your gene of interest and his neighbouring genes

Installation

To get the tool clone the git repository::

git clone https://github.com/SuleimanovShakir/SequenceMaster.git && cd SequenceMaster

Usage

SequenceMaster consits of 2 independent scripts: sequence_tools and bio_files_processor. sequence_tools mostly aimed to work with your sequence as well as filtering data from FASTQ. bio_files_processor helps you to manipulate with FASTQ and extract data from GBK.

Nucleic acids. Sequence_tools.

As we live in the world of central dogma of molecular biology, this function checks is the sequence DNA or RNA. This is an important limit because some of the functions may use only DNA sequence in it's work.

To start working with nucleic acids, just run this command:

nucleic_acid_tools(*sequences: str, action: str)

Firstly, you have to enter your DNA or RNA sequences just as 'str' type as positional arguments
Last arguments is always an action that you prefer to perform to your sequences. Here is a list of possible actions

Supported Actions:
- "transcribe": Transcribes DNA sequence to RNA sequence.
- "reverse": Reverses DNA or RNA sequences.
- "complement": Makes the complement sequence. Takes only DNA sequences.
- "reverse_complement": Gives reversed and complement to inputed DNA sequence.
- "make_binary": Recodes DNA or RNA sequence in binary code.First number is always reffered to nucleic acid type: 0 - DNA, 1 - RNA.

Proteins. Sequence_tools.

To start working with proteins, just run this command:

protein_tools(*sequences: str, action: str)

Firstly, you have to enter your protein sequence just as 'str' type as positional arguments. You have to use one-letter coding.
Last arguments is always an action that you prefer to perform to your sequences. Here is a list of possible actions

Supported Actions:
- "get_pI": Calculate isoelectric points for each amino acid in the sequence.
- "calculate_aa_freq": Calculate the frequency of each amino acid in a protein sequence.
- "translate_protein_rna": Translate amino acid sequence to RNA, using _*random codons*_ for each amino acid.
- "three_letter_code": Convert one-letter amino acid sequence to three-letter coding.
- "protein_mass": Calculate the molecular weight of the protein sequence.

FASTQ. Sequence_tools.

To start filtering your FASTQ files, just run this command fastq_filter:

fastq_filter(input_path: str = None, output_filename: str = None, 
gc_bound: Union[tuple, int, float] = (0, 100), length_bound: tuple = (0, 2**32), 
quality_threshold: Union[int, float] = 0) -> None

List of positional arguments:

input_path (str): full path to the file that you want to work with is mandatory
output_filename (str): enter just a name of the file, don't add extention!

List of keyword arguments:

gc_bound: tuple of required range of GC percentage (inclusive), num or float if only higher border of the range is needed (exclusive). (0,100) is a defaul range of GC content.
length_bound: tuple of required range of sequence length (inclusive). (0,2**32) is a defaul range of length.
quality_threshold: int of lowest level of Q-score (inclusive). 0 is a default Q-score

There is only one action - filter input FASTA by this parameters and give back filtered FASTQ file. This would be saved to fastq_filtrator_resuls subfolder. Please, provide name for the output file, otherwise it will be saved with the name of the input file.

FASTA. Bio_files_processor.

To convert multiline FASTA to oneline format, one may run convert_multiline_fasta_to_oneline:

convert_multiline_fasta_to_oneline(input_fasta: str, output_fasta: str = None) -> None:

This function converts multiline FASTA to oneline FASTA

List of positional arguments:

input_path (str): full path to the file that you want to work with is mandatory
output_filename (str): enter just a name of the file, don't add extention

As an output, user gets converted file in FASTA format, which is saved to one_line_results subfolder. Please, provide name for the output file, otherwise it will be saved with the name of the input file.

To shift starting position of your FASTA sequence, user may try change_fasta_start_pos. This function work only with oneline FASTA:

change_fasta_start_pos(input_fasta: str, shift: int, output_fasta: str = None) -> None:

This function shifts sequence to n positions from the start. But nothing is deleted! Part of sequence which is now goes before shift is located in the end of the new sequence

List of positional arguments:

input_path (str): full path to the file that you want to work with is mandatory
shift (int): the number of nucleotides by which the starting position in the file must be shifted
output_filename (str): enter just a name of the file, don't add extention

As an output, user gets fixed file in FASTA format, which is saved to change_pos_results subfolder. Please, provide name for the output file, otherwise it will be saved with the name of the input file.

GBK. Bio_files_processor.

To exctract names and translation for your genes of interest and their neibourhing genes, one may definitely use select_genes_from_gbk_to_fasta:

select_genes_from_gbk_to_fasta(input_gbk: str, output_fasta: str = None, 
*, genes_of_interest: list, n_before: int = 1, n_after: int = 1) -> None:

This function uses gbk database files to extract FASTA sequence of proteins. User enters name of interested genes and how much genes before and after this gene of interest he want to extract with proteins sequences for these genes.

Arguments (positional):

input_gbk (str): full path to the file that you want to work with is mandatory
output_fasta (str): enter just a name of the file, don't add extention!

Arguments (keyword):

genes_of_interest (list): list of gene names user is interested in
n_before (int): how many of genes before particular genes you want to extract
n_after (int): how many of genes after particular genes you want to extract

As an output, user gets fixed file in FASTA format, which is saved to gbk_fasta_resuls subfolder. Please, provide name for the output file, otherwise it will be saved with the name of the input file.

Examples

Nucleic acids tools

print(nucl_acid_tools('ATG', action='transcribe')) -> 'AUG'
print(nucl_acid_tools('ATG', 'GAT', action='reverse')) -> ['GTA', 'TAG']
print(nucl_acid_tools('ATG', 'tAg', 'AAA', action='complement')) -> ['TAC', 'aTc', 'TTT']
print(nucl_acid_tools('ATG', 'tAg', 'AAA', action='reverse_complement')) -> ['CAT', 'cTa', 'TTT']
print(nucl_acid_tools('ATG', action='make_binary')) -> '0,0,0,0,1,1,0'

Proteins tools

print(protein_tools('KKLMN', action='calculate_aa_freq')) -> {'K': 2, 'L': 1, 'M': 1, 'N': 1}
print(protein_tools('KLMN','PRST', action='translate_protein_rna')) -> ['AAGCUAAUGAAC', 'CCAAGGAGCACG']
print(protein_tools('KLMN', 'pRsT', action='three_letter_code')) -> ['Lys-Leu-Met-Asn', 'Pro-Arg-Ser-Thr']
print(protein_tools('KLMN', action='protein_mass')) -> 486.26244

FASTQ filter

fastq_filter(INPUT_FASTQ, 'filtered_fastq', gc_bound=(40,60), length_bound=(0, 200), quality_threshold=25) -> "Filtered FASTA is written!"

FASTA to oneline

convert_multiline_fasta_to_oneline(INPUT_FASTA, 'oneline_fasta') -> "Multiline FASTA is converted to oneline!"

FASTA shift start

change_fasta_start_pos(INPUT_ONELINE_FASTA, 3, 'shifte_fasta') -> "Starting position in FASTA is shifted!"

GBK extract

select_genes_from_gbk_to_fasta(INPUT_GBK, 'genes_of_interest', genes_of_interest=['mngA', 'araE', 'trpA'], n_before=4, n_after=5) -> "Genes of interest with their sequences are extracted from GBK to FASTA!":

Troubleshooting

Type of the problem	Probable cause
ValueError: No such action: {action}	You have entered a wrong action. Please, check function docstring
ValueError: Your sequence is empty	You have entered empty sequence. Please notice, this error occurs only when you enter 1 sequence.
Working with protein
ValueError: Sequence is not a protein, input should be protein	You have entered a wrong sequence
Working with nucleic acids
ValueError: Sequence is not a DNA, input should be DNA	You have entered a wrong sequence
ValueError: Sequence is not a DNA/RNA, input should be DNA/RNA	You have entered a wrong sequence
Working with FASTQ
ValueError: There are no fastq sequences	Your FASTQ input is empty
ValueError: Your arguments are not suitable!	You enter wrong type of arguments Please, check function docstring
TypeError: takes from 0 to 1 positional arguments but n were given	Sequences are not collected into the list type
ValueError: You didn't enter any PATH to file	Please, provide full path to your file
Working with FASTA
ValueError: You didn't enter any PATH to file	You have entered a wrong sequence
ValueError: Shift arguments has to be numeric	Please, enter shift arguments in numeric type
Working with GBK
ValueError: Your arguments are not in suitable type	You enter wrong type of arguments
ValueError: You have entered an empty list of genes	Please, check that your list of genes is not empty
ValueError: You didn't enter any PATH to file	Please, provide full path to your file

Contacts

Shakir Suleimanov,
Please, do not hesitate to contact me via Git-Hub or e-mail.