shmir.data package¶
Submodules¶
shmir.data.models module¶
- class shmir.data.models.Backbone(**kwargs)¶
Bases: sqlalchemy.ext.declarative.api.Base
Backbone class with information about miRNA scaffolds
- active_strand¶
- flanks3_a¶
- flanks3_s¶
- flanks5_a¶
- flanks5_s¶
- generate_regexp()¶
Function creates regexps based on active_strand and saves it to the database.
- active_strand: if is equal to 3, function use miRNA_a;
- if is equal to 1 or 5, function use miRNA_s if is equal to 0, function use both
- classmethod generate_regexp_all()¶
Function takes all objects from the database and creates regular expressions for each.
- homogeneity¶
- id¶
- loop_a¶
- loop_s¶
- miRBase_link¶
- miRNA_a¶
- miRNA_end_3¶
- miRNA_end_5¶
- miRNA_length¶
- miRNA_max¶
- miRNA_min¶
- miRNA_s¶
- name¶
- regexp¶
- siRNA1 = None¶
- siRNA2 = None¶
- structure¶
- template()¶
Returns the template of DNA (sh-miR)
siRNA1 and siRNA2 are siRNA strands and they must be initialized before using this method
- Returns:
- Sequence of sh-miR molecule on the base of chosen miRNA scaffold
- class shmir.data.models.Immuno(**kwargs)¶
Bases: sqlalchemy.ext.declarative.api.Base
Immuno motives class
- classmethod check_is_in_sequence(input_sequence)¶
Checks if input sequence conteins sequences from immuno database
- Args:
- input_sequence: RNA sequence of about 20nt length
- Returns:
- Bool if the input_sequence contains immunostimulatory motifs
- id¶
- link¶
- receptor¶
- sequence¶
shmir.data.ncbi_api module¶
- shmir.data.ncbi_api.get_data(transcript, database='nucleotide', email='amupoznan@gmail.com')¶
Function responsible to get data from given ncbi database.
- Args:
- email(str): Email to authorization with ncbi. transcript(str): Transcript to search. database(str): Name of database from ncbi. ids(list of str): List of ids to search.
- shmir.data.ncbi_api.get_mRNA(transcript, database='nucleotide', email='amupoznan@gmail.com')¶
Function to connect with NCBI database and get transcript by name
- Args:
- transcript(str): name of transcript (from NCBI) database: name of database in which we look for (default “nucleotide”) email(str): email to which NCBI needs to validate
- Returns:
- mRNA(str)
- Raises:
- NoResultError