Codons API

Codons()

The data environment, in a Python IDE, is defined:

import codons
cd = codons.Codons(sequence = None, codons_table = 'standard', amino_acids_form = 'one_letter', hyphenated = None, verbose = False, printing = True)

  • sequence str: optionally specifies the genetic sequence that will be processed through subsequent functions. The sequence can alternatively be provided ad hoc to each function.

  • codons_table str: specifies the framework for translating codons into amino acids, where the standard translation table is used by default.

  • amino_acids_form str: specifies whether the amino acid full_name, three_letter, or one_letter nomenclature will be used in the protein sequence.

  • hyphenated bool: specifies whether amino acid residues of the protein sequence are delimited by hyphens, where None defaults to True for amino_acids_form = full_name and amino_acids_form = three_letter and False for amino_acids_for = one_letter.

  • verbose & printing bool: specifies whether troubleshooting information or results will be printed, respectively.

read_fasta()

A FASTA-formatted file is parsed into the constituent sequences and descriptions:

sequences, descriptions, fasta_file = cd.read_fasta(fasta_path = None, fasta_link = None):

  • fasta_path str: The path to a FASTA file that will be loaded, parsed, and returned.

  • fasta_link str: The URL link to a FASTA file that will be imported, parsed, and returned.

Returns:

  • sequences & descriptions list: The sequences and descriptions that are contained within the FASTA file.

  • fasta_file str: The original FASTA file as a string.

make_fasta()

A simple function that constructs, returns, and optionally exports a FASTA-formatted file from the parameterized description and sequence:

fasta_file = cd.make_fasta(sequence, description = 'sequence', export_path = None):

  • sequence str: The genetic or protein sequence that will constitute the FASTA file.

  • description str: A description of the sequence that will be the first line of the FASTA file, which is appended with the length of each respective sequence in the FASTA file.

  • export_path str: The path to which the FASTA file will be exported, where None specifies that the file will not be exported.

Returns:

  • fasta_file str: The generated FASTA file.

complement()

A simple function that constructs and returns the complementary strand for a parameterized genetic sequence:

fasta_file = cd.complement(sequence = None, dna = True):

  • sequence str: The genetic sequence for which the complemenentary strand will be determined.

  • dna bool: specifies whether the parameterized strand is DNA or RNA.

Returns:

  • complementary_strand str: The complementary genetic sequence.

transcribe()

A genetic sequence is converted from DNA -> RNA, or RNA -> DNA, where the directionality of the conversion is automatically listed in the FASTA description:

transcribed_sequence = cd.transcribe(sequence = None, description = '', fasta_path = None, fasta_link = None)

  • sequence str: The genetic seqeuence that will be transcribed. The sequence is case-insensitive, and can even possess line numbers or column-spaces, which the code ignores. The parameterization of None defaults to the sequence that was initially loaded into the Codons object.

  • description str: A description of the genetic sequence that will be added to the FASTA-formatted output of the function.

  • fasta_path & fasta_link str: The path or URL link to a FASTA file that will be transcribed.

Returns:

  • transcribed_sequence str: The translated sequence.

find_start()

Determines the index of the next start codon:

index = cd.find_start(i, sequence):

  • i int: The string index of the sequence after which a start codon will be searched.

  • sequence str: The genetic sequence in which the start codon will be search.

Returns:

  • index int: The index of the next start codon.

translate()

A genetic sequence is translated into proteins that is coded by the genetic code:

proteins = cd.translate(sequence = None, fasta_path = None, fasta_link = None, organism = 'bacteria', start_codons = None, all_possible_proteins = False,
                        open_reading_frames = True,  filter_protein_size = 30, sense_strand_translation = False)

  • sequence str: The genetic sequence , of either DNA or RNA, that will be translated into a protein sequence. The sequence is case-insensitive, and can even possess line numbers or column-spaces, which the code ignores. The absence of a passed sequence executes the sequence that is loaded into the Codons object.

  • fasta_path & fasta_link str: The path or URL link to a FASTA file that will be translated.

  • organism str: specifies the type of organism whose genome is being translated, which informs which set of default start codons will be used: ['ATG', 'AUG', 'GTG', "GUG"] for bacteria or ['ATG', 'AUG'] for virus.

  • start_codons list: specifies the start codons that will be used, where None defaults to those from the organism selection.

  • all_possible_proteins bool: specifies whether all possible proteins from a given genetic sequence will be translated, instead of linearly reading the sequence.

  • open_reading_frames bool: specifies whether each of the three possible open reading frames for a specified sequence will be translated. The resultant proteins will be distinguished in their description for what open reading frame generated their translation.

  • filter_protein_size int: specifies the peptide length below which a translated peptide will be excluded from the set of predicted proteins.

  • sense_strand_translation bool: specifies whether the sense strand, complementary to the parameterzied sequence, will be translated as well.

blast_protein()

A protein sequence or a FASTA-formatted file of protein sequences is searched in through the BLAST database of the NIH for information about the protein(s):

protein_blast_results = cd.blast_protein(sequence = None, database = 'nr', description = 'Protein sequence description',  fasta_path = None, fasta_link = None,  export_name = 'codons-BLASTp', export_directory = None)

  • sequence str: The protein sequence that will be searched through the BLAST database. The sequence is case-insensitive, and can even possess line numbers or column-spaces. The sequence must be < 1000 amino acids in length.

  • database str: The BLAST database that will be searched for the protein sequence. Permissible options include: nr, refseq_select, refseq_protein, landmark, swissprot, pataa, pdb, env_nr, tsa_nr.

  • description str: A description of the protein sequence that will be added to the FASTA-formatted output.

  • fasta_path & fasta_link str: The path or URL link to a protein FASTA or multi-FASTA file that will be systematically searched.

  • export_name & export_directory str: The name of the folder and directory to which the scraped BLAST data will be saved in iterations of protein_blast_results.xml XML files. The None values enable the code to construct a unique folder name that describes the contents and saves it to the current working directory.

Returns

  • protein_blast_results list: The BLAST search results, which can be further investigated by the Bio.Blast.NCBIXM API.

blast_nucleotide()

A genetic sequence or a FASTA-formatted file of genetic sequences is searched though the BLAST database of the NIH for information about the sequence(s):

nucleotide_blast_results = cd.blast_nucleotide(sequence = None, database= 'nt', description = 'Genetic sequence description', fasta_path = None, fasta_link = None, export_name = 'codons-BLASTn', export_directory = None)

  • sequence str: The genetic sequence, of either DNA or RNA, that will be searched through BLAST. The sequence is case-insensitive, and can even possess line numbers or column-spaces, which the code ignores. The absence of a passed sequence executes the sequence that is loaded into the Codons object.

  • database str: The BLAST database that will be searched for the nucleotide sequence. Permissible options include: nr, nt, refseq_select, refseq_rna, refseq_representative_genomes, wgs, refseq_genomes, est, SRA, TSA, HTGS, pat, pdb, RefSeq_Gene, gss, dbsts.

  • description str: A description of the genetic sequence that will be added to the FASTA-formatted output of the function.

  • fasta_path & fasta_link str: The path or URL link to a genetic FASTA or multi-FASTA file that will be systematically searched.

  • export_name & export_directory str: The name of the folder and directory to which the scraped BLAST data will be saved in a file: nucleotide_blast_results.xml. The None values enable the code to construct a unique folder name that describes the contents and saves it to the current working directory.

Returns

  • nucleotide_blast_results list: The BLAST search results, which can be further investigated by the Bio.Blast.NCBIXM API.

export()

Any sequences from the aforementioned functions, which reside in the Codons object, are exported as separate files in the same folder:

cd.export(export_name = None, export_directory = None)

  • export_name str: optionally specifies a name for the folder of exported content, where None enables the code to design a unique folder name for simulation and descriptive tags of its content.

  • export_directory str: optionally specifies a path to where the folder will be exported, where None selects the current working directory.

Accessible content

The Codons object retains numerous components that are accessible to the user:

  • genes dict: A dictionary of all genes in the genetic sequence, with sub-content of a) the list of all of its Codons; and b) its protein sequence and mass.

  • protein_fasta & gene_fasta str: Assembled FASTA-formatted files for the translated proteins of a parameterized genetic sequence and for the parameterized genetic sequence, respectively.

  • transcribed_sequence & sequence str: The transcribed genetic sequence from the transcription() function and the genetical sequence that is used in any of the Codons functions, respectively.

  • amino_acid_synonyms dict: The synonyms for each amino acid, with keys of the full amino acid name.

  • codons_table & changed_codons dict: The translation table between genetic codons and amino acid residues, which is accessed with case-insensitivity, and changed codon meanings in that table by the user, respectively.

  • missed_codons dict: A collections of the codons that were parsed yet were not identified by the codons_table.

  • paths & parameters dict: Collections of the paths and parameters are defined during use of Codons.

  • export_path str: The complete export path for the Codons contents.

  • protein_blast_results & nucleotide_blast_results list: The BLAST search results for searched proteins and nucleotides, respectively, which can be further investigated by the Bio.Blast.NCBIXM API.