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Update bam insert statement to include new required data #33

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Update bam insert statement to include new required data #33

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665f088
Update bam insert statement to include new required data
mellypop Sep 20, 2022
eff825d
Add missing comma
mellypop Sep 30, 2022
c088915
Merge branch 'master' into feature/update-bam-insert-statements
mellypop Oct 5, 2022
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20 changes: 13 additions & 7 deletions src/main/scripts/add_bam_pair_xenocp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ def add_bam_pair_stp(raptr, sample, target, project, subproject, **kwargs):
None
"""
# Get stp ID
query = """select sample_target_project_id from sample_target_project_view where
query = """select sample_target_project_id from sample_target_project_view where
formal_name = %s and target_name = %s and project_name = %s and subproject = %s;"""
stp_id = raptr.fetch_item_or_fail(query, (sample, target, project, subproject))

Expand All @@ -109,19 +109,25 @@ def add_bam_pair_stp(raptr, sample, target, project, subproject, **kwargs):
# Get genome for old bam
query = """select genome_id from bam where bam_id = %s;"""
genome_id = raptr.fetch_item_or_fail(query, (bam_id,))

# Get anls type named xenocp
query = """select anls_type_id from raptr.anls_type where name='%s'"""
anls_type_id = raptr.fetch_item_or_fail(query, ('xenocp',))

# Add a new bam
query = """insert into bam (bam_id, bam_tpl_id, status, notes, genome_id)
values (nextval('blt_id_seq'), %s, 'Normal', NULL, %s) returning bam_id;"""
bam_id_xenocp = raptr.fetch_item_or_fail(query, (bam_tpl_id_xenocp, genome_id))
query = """insert into bam (bam_id, bam_tpl_id, status, notes, genome_id, anls_type_id, source_bam_id)
values (nextval('blt_id_seq'), %s, 'Normal', NULL, %s, %s, %s) returning bam_id;"""
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bam_id_xenocp = raptr.fetch_item_or_fail(query, (bam_tpl_id_xenocp, genome_id, anls_type_id, bam_id))

# Update primary_bam_id of bam_tpl with the qualifier
query = """update bam_tpl set primary_bam_id = %s where bam_tpl_id = %s;"""
raptr.execute(query, (bam_id_xenocp, bam_tpl_id_xenocp))

# Get read_group_ids and insert into bam_read_group
query = """SELECT read_group_id, pu from read_group inner join (select loadable_id as lid,
query = """SELECT read_group_id, pu from read_group inner join (select loadable_id as lid,
project_id as pid, project_name, subproject, target_name from loadable inner join
(select * from sample_target_project_view where
formal_name = %s and target_name = %s and project_name = %s
formal_name = %s and target_name = %s and project_name = %s
and subproject = %s) using (sample_target_id))
on loadable_id = lid and project_id = pid where status = 'Normal';"""
res = raptr.execute_fetch(query, (sample, target, project, subproject))
Expand Down Expand Up @@ -150,7 +156,7 @@ def add_bam_pair_bam_id(raptr, bam_id, **kwargs):
None
"""
query = """select formal_name, target_name, project_name, subproject from sample_target_project_view inner join
(select sample_target_project_id from bam_and_tpl where bam_id = %s and bam_status = 'Normal'
(select sample_target_project_id from bam_and_tpl where bam_id = %s and bam_status = 'Normal'
and legacy = false)
using (sample_target_project_id);"""
(sample, target, project, subproject) = raptr.fetch_row_or_fail(query, (bam_id,))
Expand Down