trna

Represents a collection of data about a tRNA feature that are commonly used to maintain and update SEA-PHAGES phage genomics data.

class pdm_utils.classes.trna.Trna

Bases: object

check_amino_acid_correct(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the amino acid that has been annotated for this tRNA agrees with the Aragorn and/or tRNAscan-SE prediction(s). :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_amino_acid_valid(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the amino acid that has been annotated for this tRNA is in the set of amino acids that we have opted to allow in the MySQL database. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_anticodon_correct(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the annotated anticodon agrees with the prediction by Aragorn or tRNAscan-SE. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_anticodon_valid(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the anticodon conforms to the expected length (2-4) and alphabet (“a”, “c”, “g”, “t”) or is “nnn”. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_attribute(attribute, check_set, expect=False, eval_id=None, success='correct', fail='error', eval_def=None)

Checks whether the indicated feature attribute is present in the given check_set. Uses expect to determine whether the presence (or lack thereof) is an error, or correct. :param attribute: the gene feature attribute to evaluate :type attribute: str :param check_set: set of reverence values :type check_set: set :param expect: whether the attribute’s value is expected to be in the reference set :type expect: bool :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_compatible_gene_and_locus_tag(eval_id=None, success='correct', fail='error', eval_def=None)

Check that gene and locus_tag attributes contain identical numbers. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_coordinates(eval_id=None, success='correct', fail='error', eval_def=None)

Parameters

• eval_id (str) – unique identifier for the evaluation

• success (str) – status if the outcome is successful

• fail (str) – status if the outcome is unsuccessful

• eval_def (str) – description of the evaluation

Returns

check_gene_structure(eval_id=None, success='correct', fail='error', eval_def=None)

Check that the gene qualifier contains an integer. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_length(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the tRNA is in the expected range of lengths. The average tRNA gene is 70-90bp in length, but it is not uncommon to identify well-scoring tRNAs in the 60-100bp range. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_locus_tag_structure(check_value=None, only_typo=False, prefix_set={}, case=True, eval_id=None, success='correct', fail='error', eval_def=None)

Check if the locus_tag is structured correctly.

Parameters

• check_value (str) – Indicates the genome id that is expected to be present. If None, the ‘genome_id’ parameter is used.

• only_typo (bool) – Indicates if only the genome id spelling should be evaluated.

• prefix_set (set) – Indicates valid common prefixes, if a prefix is expected.

• case (bool) – Indicates whether the locus_tag is expected to be capitalized.

• eval_id – same as for check_attribute().

• success – same as for check_attribute().

• fail – same as for check_attribute().

• eval_def – same as for check_attribute().

check_magnitude(attribute, expect, ref_value, eval_id=None, success='correct', fail='error', eval_def=None)

Check that the magnitude of a numerical attribute meets expectations. :param attribute: the gene feature attribute to evaluate :type attribute: str :param expect: symbol designating direction of magnitude (>=<) :type expect: str :param ref_value: numerical value for comparison :type ref_value: int, float, datetime :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_note_structure(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the note field is formatted properly.

Genbank does not enforce any standard for the note field. This means that a note does not have to exist.

SEA-PHAGES note fields should look like ‘tRNA-Xxx(nnn)’. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_orientation(fmt='fr_short', case=True, eval_id=None, success='correct', fail='error', eval_def=None)

Check that the orientation is set appropriately. :param fmt: indicates how coordinates should be formatted :type fmt: str :param case: indicates whether orientation data should be cased :type case: bool :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_orientation_correct(fmt='fr_short', case=True, eval_id=None, success='correct', fail='error', eval_def=None)

Check that the orientation agrees with the Aragorn and/or tRNAscan-SE predicted orientation. If Aragorn/tRNAscan-SE report a forward orientation, it means they agree with the annotated orientation. If they report reverse orientation, they think the annotation is backwards. :param fmt: indicates how coordinates should be formatted :type fmt: str :param case: indicates whether orientation data should be cased :type case: bool :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_product_structure(eval_id=None, success='correct', fail='error', eval_def=None)

Checks that the product field is formatted properly, and that the annotated amino acid is valid. Genbank enforces that all tRNA annotations that have a product field have it annotated as either ‘tRNA-Xxx’, where Xxx is one of the 20 standard amino acids, or ‘tRNA-OTHER’ for those tRNAs which decode a non-standard amino acid (e.g. SeC, Pyl, fMet). SEA-PHAGES may also append the anticodon parenthetically for a product field such as ‘tRNA-Xxx(nnn)’. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_sources(eval_id=None, success='correct', fail='error', eval_def=None)

Check that this tRNA’s DNA sequence can successfully turn up a tRNA when run through Aragorn and tRNAscan-SE. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

check_terminal_nucleotides(eval_id=None, success='correct', fail='warning', eval_def=None)

Checks that the tRNA ends with “CCA” or “CC” or “C”. :param eval_id: unique identifier for the evaluation :type eval_id: str :param success: status if the outcome is successful :type success: str :param fail: status if the outcome is unsuccessful :type fail: str :param eval_def: description of the evaluation :type eval_def: str :return:

create_seqfeature(type, start, stop, strand)

get_begin_end()

Accesses feature coordinates in transcription begin-end format. :return: (begin, end)

get_qualifiers(type)

Helper function that uses tRNA data to populate the qualifiers attribute of seqfeature. :return: qualifiers OrderedDict()

parse_amino_acid()

Attempts to parse the amino_acid attribute from the product and note attributes. :return:

parse_anticodon()

Attempts to parse the anticodon attribute from the note attribute. :return:

reformat_start_and_stop(fmt)

Convert existing start and stop coordinates to the indicated new format; also updates the coordinate format attribute to reflect any change. :param fmt: the new desired coordinate format :type fmt: str :return:

run_aragorn()

Uses an AragornHandler object to negotiate the flow of information between this object and Aragorn. :return:

run_trnascanse()

Uses a TRNAscanSEHandler object to negotiate the flow of information between this object and tRNAscan-SE. :return:

set_amino_acid(value)

Sets the amino_acid attribute using the indicated value. :param value: the Amino acid to be used :type value: str :raise: ValueError :return:

set_anticodon(value)

Sets the anticodon attribute using the indicated value. :param value: the anticodon to use for this tRNA :type value: str :return:

set_eval(eval_id, definition, result, status)

Constructs and adds and Evaluation object to this feature’s list of evaluations. :param eval_id: unique identifier for the evaluation :type eval_id: str :param definition: description of the evaluation :type definition: str :param result: description of the evaluation outcome :type result: str :param status: overall outcome of the evaluation :type status: str :return:

set_gene(value, delimiter=None, prefix_set=None)

Set the gene attribute. :param value: Gene data to parse. Also passed to set_num(). :type value: str :param delimiter: Passed to set_num(). :type delimiter: str :param prefix_set: Passed to set_num(). :type prefix_set: set

set_location_id()

Create identifier tuples containing feature location data. For this method we only care about gene boundaries and will ignore any multi-part elements to the gene. :return:

set_locus_tag(tag='', delimiter='_', check_value=None)

Populate the locus_tag and parse the locus_tag number. :param tag: Input locus_tag data :type tag: str :param delimiter: Value used to split locus_tag data :type delimiter: str :param check_value: Genome name or other value that will be used to parse the locus_tag to identify the feature number :type check_value: str

set_name(value=None)

Set the feature name. Ideally, the name of the CDS will be an integer. This information can be stored in multiple fields in the GenBank-formatted flat file. The name is derived from one of several qualifiers. :param value: Indicates a value that should be used to directly set the name regardless of the ‘gene’ and ‘_locus_tag_num’ attributes. :type value: str

set_nucleotide_length(use_seq=False)

Set the nucleotide length of this gene feature. :param use_seq: whether to use the Seq feature to calculate nucleotide length of this feature :type use_seq: bool :return:

set_nucleotide_sequence(value=None, parent_genome_seq=None)

Set this feature’s nucleotide sequence :param value: sequence :type value: str or Seq :param parent_genome_seq: parent genome sequence :type parent_genome_seq: Seq :raise: ValueError :return:

set_num(attr, description, delimiter=None, prefix_set=None)

Set a number attribute from a description. :param attr: Attribute to set the number. :type attr: str :param description: Description data from which to parse the number. :type description: str :param delimiter: Value used to split the description data. :type delimiter: str :param prefix_set: Valid possible delimiters in the description. :type prefix_set: set

set_orientation(value, fmt, case=False)

Set the orientation based on the indicated format. :param value: orientation value :type value: int or str :param fmt: how orientation should be formatted :type fmt: str :param case: whether to capitalize the first letter of orientation :type case: bool :return:

set_seqfeature(type=None)

Create a SeqFeature object with which to populate the seqfeature attribute. :return:

set_structure(value)

Set the secondary structure string so downstream users can easily display the predicted fold of this tRNA. :param value: the string to use as the secondary structure :type value: str :return: