sequence_Helicopter

A bioinformatics tool that performs basic operations on DNA and RNA sequences and filters sequences in FASTQ format files

Installing and Running Programs

Run the following commands to start it:

git clone [email protected]:hosp54/sequence_Helicopter.git

python sequence_helicopter.py

If you encounter the error of importing additional functions, try moving the files dna_rna_operations.py and gc_and_quality_calculator.py into the same folder as sequence_helicopter.py.

System requirements: Python 3.10 and above

Function description

Two main functions

• filter_fastq -filters FASTQ sequences using the following parameters: percentage of GC composition, sequence length, average number of reads.

• The parameters are set by default, but the user can enter the required parameter values.

  Accepts as input a dictionary, a FASTQ format file. Returns FASTQ file with filtered sequences.

  Arguments: input_fastq (path to the FASTQ file you want to run through sequence Helicopter) output_fastq (path to save the FASTQ file with the filtering results) length_bounds (tuple of minimum and maximum sequence lengths) quality_threshold (average sequence quality threshold).

• run_dna_rna_tools - Converts DNA or RNA sequences. It takes a list of sequences as input and one of four commands as the last argument: transcribe, reverse, complement or reverse_complement.

Additional functions for filter_fastq (gc_and_quality_calculator)

• calculate_gc_content - calculates the percentage of GC content in the sequence.
• calculate_quality - calculates the average quality of the sequence over the string of qualities.

Additional functions for filter_fastq (fastq_reader)

• fastq_to_dict - Converts a FASTQ file into a dictionary for the filter_fastq.
• write_fast - Writes filtered sequences (dictionary) to a FASTQ file.

Additional functions for run_dna_rna_tools (dna_rna_operations)

• transcribe - performs transcription from DNA to RNA.
• reverse - unfolds sequences.
• complement - returns complementary DNA or RNA sequences (if the sequence contains T and U at the same time - an error will be reported).
• reverse_complement - returns complementary DNA or RNA sequences and unfolds them.

New tool in the sequence_Helicopter family - bio_files_processor

Additional functions for bio_files_processor

• convert_multiline_fasta_to_oneline - Converts a multi-line FASTA file into a single-line format for each sequence. Arguments: input_fasta -- the path to the input FASTA file (str). output_fasta -- the path to the output FASTA file (str). If not provided, a new filename will be created by appending '_oneline' to the input file's name (default is None).

• parse_blast_output - Parses a BLAST output file to extract the first (first == best) matching description for each query and sorts these descriptions alphabetically.

  Arguments: input_file -- the path to the input BLAST output file (str). output_file -- the path to the output file where sorted descriptions will be written (str).

  Contacts

  [email protected] (Ivan)