Biomolecule manager

Contains tools for working with proteins, nucleic acids and fastq data sorting

Import biomolecules_manager library, then you can call functions with certain arguments:

• dna_rna_tools
• fastq_tools
• protein_tools
  Read about each function below

DNA-RNA tools

Provide the function arguments:

1. the first argument should be command (choose one of: transcribe, reverse, complement, reverse_complement)
2. other arguments should be the sequencee(s) of the nucleic acid(s)

Here is the catalogue of actions the user can choose:

• transcribe - makes transcribed RNA or DNA(reversed transcription) chain
• complement - returns complement chain(s) for DNA sequences
• reverse - makes reversed chain(s)
• reverse_complement - gives reversed complement sequense(s) of DNA chain

Protein tools

Provide the tool with the sequence(s) of the protein(s) in 1-letter format (for example, DYKDDDDK) and the function needed. If you occasionally write down a non-peptide sequence, the programm will return an error.

Here is the catalogue of actions the user can choose:

• count_length: gives the length(s) of the protein sequence(s)
• count_nucleotide_length: counts the length(s) of the coding nucleotide sequence(s) of the protein sequence(s)
• count_molecular_mass: calculates molecular mass of the input (the algorithm takes into consideration water mass and subtracts it)
• show_content: shows the aminoacid content of the protein(s)
• convert_1_to_3: converts 1-letter format into 3-letter one
• count_extinction_280nm: counts the molar extinction coefficient (this function counts cystine contribution to extinction coefficient as two cysteins give 1 SS-bond)

Fastq tools

Filters the sequences suitable for given bounds. Arguments: Accept sequences from fastq files as set. Example:{'name of read': ('nucleic acid sequence', 'corresponding quality of read')} Parameters can be set using nominal variables

Here is the catalogue of actions the user can set: gc_bounds = (y, x) or gc_bounds = x

• filters values between 0 and x (doesn't include x) if input is int
• filters values between y and x (doesn't include x) if input is tuple
• default - (0, 100)

length_bounds = (y, x) or length_bounds = x

• filters values between 0 and x (doesn't include x) if input is int
• filters values between y and x (doesn't include x) if input is tuple
• default - (0, 2 ** 32)

quality_thresold

• filters values higher then given (int)
• default - 0

Fastq tools returns the filtered set