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feat(IPVC-2425): add migration to fix tx-alt-exon-pairs view #34

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merged 2 commits into from
May 8, 2024
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feat(IPVC-2425): add migration to fix tx-alt-exon-pairs view #34

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44719c5
feat(IPVC-2425): add migration to fix tx-alt-exon-pairs view
bsgiles73 May 7, 2024
4a41d75
feat(IPVC-2425): update view where criteria
bsgiles73 May 7, 2024
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57 changes: 57 additions & 0 deletions src/alembic/versions/f885cb84efce_update_tx_alt_exon_pairs_v.py
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Original file line number Diff line number Diff line change
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"""update tx_alt_exon_pairs_v

Revision ID: f885cb84efce
Revises: 14eed54ff90d
Create Date: 2024-05-07 21:01:03.693969

"""
from typing import Sequence, Union

from alembic import op
import sqlalchemy as sa


# revision identifiers, used by Alembic.
revision: str = 'f885cb84efce'
down_revision: Union[str, None] = '14eed54ff90d'
branch_labels: Union[str, Sequence[str], None] = None
depends_on: Union[str, Sequence[str], None] = None


def upgrade() -> None:
op.execute("DROP VIEW IF EXISTS tx_alt_exon_pairs_v CASCADE;")
op.execute("""
CREATE VIEW tx_alt_exon_pairs_v AS
SELECT g.symbol, g.symbol as hgnc, g.gene_id,TES.exon_SET_id AS tes_exon_SET_id,
AES.exon_SET_id AS aes_exon_SET_id, TES.tx_ac AS tx_ac,AES.alt_ac AS alt_ac,
AES.alt_strand,AES.alt_aln_method, TEX.ORD AS ORD,TEX.exon_id AS tx_exon_id,
AEX.exon_id AS alt_exon_id, TEX.start_i AS tx_start_i,TEX.END_i AS tx_END_i,
AEX.start_i AS alt_start_i, AEX.END_i AS alt_END_i, EA.exon_aln_id,EA.cigar
FROM exon_SET tes
JOIN transcript t ON tes.tx_ac=t.ac
JOIN gene g ON t.gene_id=g.gene_id
JOIN exon_set aes ON tes.tx_ac=aes.tx_ac AND tes.alt_aln_method='transcript' AND aes.alt_aln_method !~ 'transcript'
JOIN exon tex ON tes.exon_SET_id=tex.exon_SET_id
JOIN exon aex ON aes.exon_SET_id=aex.exon_SET_id AND tex.ORD=aex.ORD
LEFT JOIN exon_aln ea ON ea.tx_exon_id=tex.exon_id AND ea.alt_exon_id=AEX.exon_id;
""")


def downgrade() -> None:
op.execute("DROP VIEW IF EXISTS tx_alt_exon_pairs_v CASCADE;")
op.execute("""
CREATE VIEW tx_alt_exon_pairs_v AS
SELECT g.symbol, g.symbol as hgnc, g.gene_id,TES.exon_SET_id AS tes_exon_SET_id,
AES.exon_SET_id AS aes_exon_SET_id, TES.tx_ac AS tx_ac,AES.alt_ac AS alt_ac,
AES.alt_strand,AES.alt_aln_method, TEX.ORD AS ORD,TEX.exon_id AS tx_exon_id,
AEX.exon_id AS alt_exon_id, TEX.start_i AS tx_start_i,TEX.END_i AS tx_END_i,
AEX.start_i AS alt_start_i, AEX.END_i AS alt_END_i, EA.exon_aln_id,EA.cigar
FROM exon_SET tes
JOIN transcript t ON tes.tx_ac=t.ac
JOIN gene g ON t.gene_id=g.gene_id
JOIN exon_set aes ON tes.tx_ac=aes.tx_ac AND tes.alt_aln_method='transcript' AND aes.alt_aln_method!='transcript'
JOIN exon tex ON tes.exon_SET_id=tex.exon_SET_id
JOIN exon aex ON aes.exon_SET_id=aex.exon_SET_id AND tex.ORD=aex.ORD
LEFT JOIN exon_aln ea ON ea.tx_exon_id=tex.exon_id AND ea.alt_exon_id=AEX.exon_id;
""")

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