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
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
receptor
sequence
class shmir.data.models.InputData(**kwargs)

Bases: sqlalchemy.ext.declarative.api.Base

Table storing input data to sh-miR algorithm

id
immunostimulatory
maximum_CG
maximum_offtarget
minimum_CG
results
scaffold
transcript_name
class shmir.data.models.Result(**kwargs)

Bases: sqlalchemy.ext.declarative.api.Base

sh-miR results table

as_json()
backbone
get_task_id()
id
input_data
input_id
pdf
score
sequence
shmir

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

Module contents