tmrna

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

class pdm_utils.classes.tmrna.Tmrna

Bases: object

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

Makes sure only one region exists for this tRNA. :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_peptide_tag_correct(eval_id=None, success='correct', fail='error', eval_def=None)

Checks whether the annotated peptide tag matches the Aragorn output. :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_peptide_tag_valid(eval_id=None, success='correct', fail='error', eval_def=None)

Checks whether the annotated peptide tag contains any letters not strictly within the protein alphabet. :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:

get_begin_end()

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

get_qualifiers()

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

parse_peptide_tag()

Parse the peptide_tag attribute out of the note field. :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:

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.

Parameters

• value (str) – Gene data to parse. Also passed to set_num().

• delimiter (str) – Passed to set_num().

• prefix_set (set) – Passed to set_num().

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()

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