How to use SQL to concatenate two rows with grouping and CASE - sql-server

Question

I have some genomic data that is in SQL Server 2016 Express and it is currently shaped in a long format with a reference genome and test genomes split by a SubjectID, genes, and codons (e.g. a 3-tuple).
What I really need is to reshape my data into one which the tuples are concatenated together but ONLY when there is a mutation (as compared to the reference genome) in the tuple. This will be a more usable format for everyone.
My data looks like this
DECLARE #myTable TABLE
(
SubjectID VARCHAR(MAX),
country VARCHAR(MAX),
gene VARCHAR(MAX),
position INT,
ReferenceNucleotide VARCHAR(1),
TestNucleotide VARCHAR(1),
codon INT,
nucleotide_order INT
)
INSERT INTO #myTable
VALUES
('1-0002','India','gyrA', 65,'A','x', 92,1),
('1-0002','India','gyrA', 66,'T','x', 92,2),
('1-0002','India','gyrA', 67,'C','C', 92,3),
('1-0002','India','gyrA', 68,'T','T', 93,1),
('1-0002','India','gyrA', 69,'A','A', 93,2),
('1-0002','India','gyrA', 70,'C','C', 93,3),
('1-0002','India','gyrA', 71,'G','G', 94,1),
('1-0002','India','gyrA', 72,'A','A', 94,2),
('1-0002','India','gyrA', 73,'C','C', 94,3),
('1-0002','India','gyrA', 74,'A','A', 95,1),
('1-0002','India','gyrA', 75,'G','C', 95,2),
('1-0002','India','gyrA', 76,'C','C', 95,3),
('1-0002','India','gyrA', 77,'C','C', 96,1),
('1-0002','India','gyrA', 78,'T','T', 96,2),
('1-0002','India','gyrA', 79,'G','N', 96,3)
However, there are a couple of conditions
If all three nucleotides are the same for the reference and test genome I want a 'WT'
If there is any difference in nucleotides, I want the 3-tuple from the test genome (in the nucleotide order)
I need to group by SubjectID and gene because I have lots of Subjects & genes
And my result would look like
1-0002 India gyrA 92 xxC
1-0002 India gyrA 93 WT
1-0002 India gyrA 94 WT
1-0002 India gyrA 95 ACC
1-0002 India gyrA 96 CTN
I can identify where the codons are that need to have the 3-tuple but am struggling with how to concatentate them
DECLARE #myCodons TABLE (SubjectID varchar(max), country varchar(max), gene varchar(max), codon int, WT int)
INSERT INTO #myCodons
SELECT
SubjectID, country, gene, codon,
SUM(CASE WHEN RefNucleotide=TestNucleotide THEN 0 ELSE 1 END) AS WT
FROM
#myTable
GROUP BY
SubjectID, country, gene, codon
SELECT *
FROM #myCodons
ORDER BY codon

Answer 1

Start with something like:
select T1.SubjectID, T1.country, T1.gene, T1.codon,
T1.RefGenome + T2.RefGenome + T3.RefGenome RefGenome,
T1.TestGenome + T2.TestGenome + T3.TestGenome TestGenome
from #myTable T1
inner join #myTable T2 on T1.SubjectID = T2.SubjectID and T1.country = T2.country
and T1.gene = T2.gene and T1.codon = T2.codon and T2.nucleotide_order = 2
inner join #myTable T3 on T1.SubjectID = T3.SubjectID and T1.country = T3.country
and T1.gene = T3.gene and T1.codon = T3.codon and T3.nucleotide_order = 3
where T1.nucleotide_order = 1
You can then build on this with case statements to work out whether to display the test genome or 'WT'

Answer 2

An alternative approach which might be of use:
select SubjectID, country, gene, codon, case when RefGenomeStr = TestGenomeStr then 'WT' else TestGenomeStr end wanted_string
from #myTable t1
cross apply(
SELECT
STUFF((
SELECT
', ' +RefGenome
FROM #myTable t2
WHERE t2.SubjectID= t1.SubjectID and t2.country = t1.country and t2.gene = t1.gene and t2.codon = t1.codon
FOR XML PATH ('')
)
, 1, 1, '')
, STUFF((
SELECT
', ' +TestGenome
FROM #myTable t2
WHERE t2.SubjectID= t1.SubjectID and t2.country = t1.country and t2.gene = t1.gene and t2.codon = t1.codon
FOR XML PATH ('')
)
, 1, 1, '')
) ca (RefGenomeStr,TestGenomeStr)
where nucleotide_order = 1
Result:
+----+-----------+---------+------+-------+---------------+
| | SubjectID | country | gene | codon | wanted_string |
+----+-----------+---------+------+-------+---------------+
| 1 | 1-0002 | India | gyrA | 92 | x, x, C |
| 2 | 1-0002 | India | gyrA | 93 | WT |
| 3 | 1-0002 | India | gyrA | 94 | WT |
| 4 | 1-0002 | India | gyrA | 95 | A, C, C |
| 5 | 1-0002 | India | gyrA | 96 | C, T, N |
+----+-----------+---------+------+-------+---------------+
Demo