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"""
Tests for methods which return collections of transcript IDs that aren't
converting from some type of name or ID.
"""
from __future__ import absolute_import
from .common import eq_
from pyensembl import cached_release
def test_transcript_support_level():
"""The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript
models for users, based on the type and quality of the alignments used to annotate the transcript.
In the Ensembl database, it can be assigned to a value 1 through 5, or reported as NA, or missing, or missing
completely in older releases. We translate it to an integer value, otherwise to None.
"""
ensembl93 = cached_release(93)
transcript = ensembl93.transcripts_by_name("DDX11L1-202")[0]
eq_(transcript.support_level, 1)
# For this transcript, the transcript_support_level value is missing in the database record:
transcript = ensembl93.transcripts_by_name("OR4G11P-202")[0]
eq_(transcript.support_level, None)
# Some features are reported as "NA" in Ensembl: those are features like pseudogenes, single exon transcripts,
# HLA, T-cell receptor and Ig transcripts that are not analysed in terms of TSL and therefore not given any
# of the TSL categories. We translate NA to None as well.
transcript = ensembl93.transcripts_by_name("MIR1302-2-201")[0]
eq_(transcript.support_level, None)
# Transcript_support_level column was missing completely in GRCh37 and older releases of GRCh38:
ensembl77 = cached_release(77)
transcript = ensembl77.transcripts_by_name("DDX11L1-002")[0]
eq_(transcript.support_level, None)
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