🧬 BioinfTools

Bioinformatics tools for working with nucleic acid or protein sequences

• Basic operations with nucleic acid sequences
• FastQC analysis
• Checking for sequence validity
• Reading bioinformatics files (fasta, fastq)

Author: Elizaveta Salnikova

Main Features

Checking for sequence validity:

Module seq_validation

• is_nucleic_acid - checks if input seq is nucleic acid
• is_dna - checks if input seq is DNA
• is_rna - checks if input seq is RNA
• length_check - checks the length of sequences list

Basic operations with nucleic acid sequences:

run_dna_rna_tools - performs basic operations with DNA or RNA sequences

• Accept any number of positional arguments
• Case-sensitive
• Accepts DNA or RNA sequences and the name of the procedure to be performed
• Returns string if a single sequence is submitted or a list of rows if several sequences are submitted

Module dna_rna_tools

• transcribe - returns RNA sequence transcribed from DNA
• reverse- returns reverse sequence
• complement - returns complement sequence
• reverse_complement - returns reverse complement sequence

FastQC analysis

filter_fastq - filters reads based on QC

• Accepts 5 arguments as input:
  • input_fastq - absolute path to fastq file with unfiltered sequences
  • output_fastq - name of fastq file with filtered sequences
  • gc_bounds - the GC percentage for filtering ((0, 100) by default)
  • length_bounds - the length interval for filtering ((0.2**32) by default)
  • quality_threshold - the threshold value of the average read quality (0 by default (phred33))
• Returns program work result information to notify user about performed operation
• Saves sequences that match all given conditions to the output_fastq file in the directory filtered

Module fastqc_tools

• check_gc_count - checks if GC percentage of the read matches given conditions
• check_len - checks if length of the read matches given conditions
• check_quality - checks if quality of the read matches given conditions
• fastq_to_dict - converts fastq file to dictionary
• save_filtered - saves filtered fastq sequences from dictionary to the file

Reading bioinformatics files

convert_multiline_fasta_to_oneline - converts multiline fasta to oneline fasta

• Accepts 2 arguments as input:
  • input_fasta - absolute path to multiline fasta file
  • output_fasta - name of resulted oneline fasta file
• Parses the input fasta file in which the sequence (DNA/RNA/protein/...) can be split into several lines and saves it to a new fasta file in which each sequence fits into one line

parse_blast_output - parses blast output file to extract the names of best matched sequences

• Accepts 2 arguments as input:
  • input_file - absolute path to blast results file
  • output_file - name of the file with names of best matched sequence for each query
• For each query selects the first row from the Description column and saves the set of obtained proteins to a new file in one column sorted alphabetically

Additional information

• Functions in modules can be used individually or as part of run_dna_rna_tools and filter_fastq
• Functions are user-friendly - prevent data loss, notify user of file overwriting risk
• Functions return program work result information to notify user about performed operation

Examples

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']

filter_fastq(input_fastq, output_fastq, gc_bounds = 60, length_bounds = (89, 100), quality_threshold = 30)
# 'Sequences are filtered out' if everything worked correctly

convert_multiline_fasta_to_oneline (input_fasta, output_fasta)
# 'Convert multiline fasta to oneline' if everything worked correctly

parse_blast_output(input_file, output_file)
# 'Extract the names of best matched sequences.' if everything worked correctly

If the output file already exists, functions will notify user before performing the operation.
#'Check the name of the output file! Risk of overwriting!'