fastq_tool (release from February 2025)

Module contains all basic procedures which could be useful in work with DNA/RNA sequences

Upd: In the last release new features were added, errors were corrected, the code was improved and optimized

New classes: RNASequence, DNASequence, AminoAcidSequence

Different procedures for DNA/RNA/aminoacid sequences are avaliable now in more convinient format!

Avaliable methods for objects of RNASequence and DNASequence classes:

• is_correct_seq: Check if all letters of your sequense are relevant to particular type of biological sequence
• reverse: Returns reverse sequence
• complement: Returns complement sequence
• reverse_complement: Return reverse complement sequence

Additional option for object of DNASequence class:

• transcribe: Return transcribed RNA sequence (object of RNASequence class)

Avaliable methods for objects of AminoAcidSequence class:

• get_mass_dalton: Returns molecular mass of given amino-acid sequence in Daltons

Example:

seq1 = DNASequence('ACGGGGTTT')
seq2 = seq1.reverse_complement()
seq3 = seq1.transcribe()

print(seq2)
print(seq3)

Output:

AAACCCCGT

UGCCCCAAA

filter_fastq

Checks the quality of FASTQ reads and filter it

Upd: In the last release errors were corrected, the code was improved and optimized. Now working time of the function is significantly lower due to BioPython package usage!

Arguments:

• input_fastq (str) - path to the input fastq file
• output_fastq (str) - path (and name) of the output fastq file (if None - filter_fastq creates an output file in the working directory) (default: None)
• gc_bounds (tuple) - limit bounds for GC% (default: (0,100)); if only one specified, it will be accepted as upper bound
• length_bounds (tuple) - limit bounds for read length (default: (0, 2**32)); if only one specified, it will be accepted as upper bound
• quality_threshold (float) - limit of mean read quality score (phred33) (default: 0)

filter_fastq creates a new file containing FASTQ sequences satisfying all conditions

Usage:

filter_fastq (input_fastq = "file.fastq", gc_bounds = 80, length_bounds = (50, 100), quality_threshold = 32)

bio_files_processor

Module contains procedures for work with "bio"-files

convert_multiline_fasta_to_oneline

Create new one-line (1 sequence in the 1 string) FASTA file from multi-line FASTA file

Arguments:

• input_fasta (str) - path to the input FASTA file
• output_fasta (str) - path (and name) of the output FASTA file (if None - convert_multiline_fasta_to_oneline creates an output file in the working directory) (default: None)

Usage:

convert_multiline_fasta_to_oneline(input_fasta = 'example_multiline_fasta.fasta')

parse_blast_output

Create new file with sorted list of proteins from BLAST-result file

Arguments:

• input_file (str) - path to the input txt file with BLAST result
• output_file (str) - path (and name) of the output file (if None - parse_blast_output creates an output file in the working directory) (default: None)

Usage:

parse_blast_output(input_file = 'example_blast_results.txt')

select_genes_from_gbk_to_fasta

Create new FASTA file with protein sequences of genes of interest in the particular interval from *.gbk file

Arguments:

• input_gbk (str) - path to the input *.gbk file with BLAST result
• genes (tuple) - names of genes of interest
• n_before (int) - number of genes before gene of interest (default: 1)
• n_after (int) - number of genes after gene of interest (default: 1)
• output_fasta (str) - path (and name) of the output file (if None - select_genes_from_gbk_to_fasta creates an output file in the working directory) (default: None)

If there are several lines with information about gene, select_genes_from_gbk_to_fasta will find nearest genes for all of them For example, your gene of interest is btuD, n_before = 4 and n_after = 3. In *.gbk file there are three btuD entries: btuD_1, btuD_2, btuD_3. In this situation select_genes_from_gbk_to_fasta will find protein sequences of 4 genes before each of (btuD_1, btuD_2, btuD_3) and of 3 genes after each of (btuD_1, btuD_2, btuD_3) including protein sequences of (btuD_1, btuD_2, btuD_3).

Usage:

select_genes_from_gbk_to_fasta(input_gbk = 'example_gbk.gbk', 
                               genes = ('dtpD', 'clpA', 'rhsD'),
                               n_before = 1, n_after = 3)