blanking out repeated columns in rows
blanking out repeated columns in rows
От:
Sean McCorkle <mccorkle@avenger.bio.bnl.gov>
Дата:
Here's one for all you SQL jockeys out there (hope this is a good group to post this query) I'm currently (happily) using PostgreSQL for doing DNA expression analysis, and I often end up with joins where columns on the left side get repeated to matching differing For example, a select output ends up looking like this: (from psql. i've removed the - and | lines) tag gb_id pos descrip ACTATTTTTAGAGACCC NM_032685.1 307 hypothetical protein MGC13005 (MGC13005), AGAAAAAAAAAAAAAAA NM_019110.2 27 hypothetical protein P1 p373c6 (P1P373C6) AGAAAAAAAAAAAAAAA NM_019110.2 27 hypothetical protein P1 p373c6 (P1P373C6) AGCCACCACGCCTGGTC NM_003693.1 260 acetyl LDL receptor; SREC=scavenger AGCCACCGCGCCCGGCC NM_007081.1 486 RAB, member of RAS oncogene family-like 2B AGCCACCGCGCCCGGCC NM_013412.1 486 RAB, member of RAS oncogene family-like 2A AGCCACCGCGCCTGGCC NM_000651.2 229 complement component (3b/4b) receptor 1, AGCCACCGCGCCTGGCC NM_000573.2 229 complement component (3b/4b) receptor 1, ATCAAAAAAAAAAAAAA NM_079421.1 25 cyclin-dependent kinase inhibitor 2D but I (and my colleagues) would much rather see this, which draws attention to the duplicates (or multiples) in the left column. tag gb_id pos descrip ACTATTTTTAGAGACCC NM_032685.1 307 hypothetical protein MGC13005 (MGC13005), AGAAAAAAAAAAAAAAA NM_019110.2 27 hypothetical protein P1 p373c6 (P1P373C6) NM_019110.2 27 hypothetical protein P1 p373c6 (P1P373C6) AGCCACCACGCCTGGTC NM_003693.1 260 acetyl LDL receptor; SREC=scavenger AGCCACCGCGCCCGGCC NM_007081.1 486 RAB, member of RAS oncogene family-like 2B NM_013412.1 486 RAB, member of RAS oncogene family-like 2A AGCCACCGCGCCTGGCC NM_000651.2 229 complement component (3b/4b) receptor 1, NM_000573.2 229 complement component (3b/4b) receptor 1, ATCAAAAAAAAAAAAAA NM_079421.1 25 cyclin-dependent kinase inhibitor 2D Is there any slick way to accomplish this in SQL? Or is there a switch or something I've missed in postgresql? Currently I'm postprocessing the output with a perl script, but I'd prefer the SQL to generate it directly, if possible. Thanks, folks! =sean ------------------------------------------------------------------------------- Sean R. McCorkle mccorkle@bnl.gov | Haven't you heard, that aside Genome Group (631) 344-4270 ph | from the details, there's Biology Department (631) 344-3407 fax | nothing further to be found? Brookhaven National Laboratory | --Master Dogen's 300 Koan Upton, New York 11973 | Shobogenzo (commentary)
Re: blanking out repeated columns in rows
От:
Masaru Sugawara <rk73@sea.plala.or.jp>
Дата:
On Tue, 7 May 2002 11:03:50 -0400
Sean McCorkle wrote:
> but I (and my colleagues) would much rather see this, which draws
> attention to the duplicates (or multiples) in the left column.
>
> tag gb_id pos descrip
>
> ACTATTTTTAGAGACCC NM_032685.1 307 hypothetical protein MGC13005 (MGC13005),
> AGAAAAAAAAAAAAAAA NM_019110.2 27 hypothetical protein P1 p373c6 (P1P373C6)
> NM_019110.2 27 hypothetical protein P1 p373c6 (P1P373C6)
> AGCCACCACGCCTGGTC NM_003693.1 260 acetyl LDL receptor; SREC=scavenger
> AGCCACCGCGCCCGGCC NM_007081.1 486 RAB, member of RAS oncogene family-like 2B
> NM_013412.1 486 RAB, member of RAS oncogene family-like 2A
> AGCCACCGCGCCTGGCC NM_000651.2 229 complement component (3b/4b) receptor 1,
> NM_000573.2 229 complement component (3b/4b) receptor 1,
> ATCAAAAAAAAAAAAAA NM_079421.1 25 cyclin-dependent kinase inhibitor 2D
How about this method of appending sequences as unique indices?
First:
create temp sequence dna_rownum1;
create temp sequence dna_rownum2;
Secand:
SELECT setval('dna_rownum1', 1, false); -- (1)
SELECT setval('dna_rownum2', 1, false); -- (2)
SELECT (CASE WHEN t1.idx = t3.idx THEN t1.tag ELSE NULL END) AS tag, t1.gb_id, t1.pos, t1.descrip FROM (SELECT *, nextval('dna_rownum1') AS idx FROM dna ORDER BY idx ) AS t1, (SELECT t2.tag, MIN(t2.idx) AS idx FROM (SELECT tag, nextval('dna_rownum2') AS idx FROM dna ORDER BY idx) AS t2 GROUP BY t2.tag ) AS t3WHERE t1.tag = t3.tagORDER BY t1.tag, t1.idx; -- (3)
Note: (1) and (2) need to be executed at the same time, but (3) doesn't. And CREATE TEMP SEQUENCE is practicable in 7.2 or later.
Regards,
Masaru Sugawara
Re: blanking out repeated columns in rows
От:
Masaru Sugawara <rk73@sea.plala.or.jp>
Дата:
On Thu, 09 May 2002 01:51:59 +0900
Masaru Sugawara wrote:
>
> How about this method of appending sequences as unique indices?
>
>
> First:
> create temp sequence dna_rownum1;
> create temp sequence dna_rownum2;
>
> Secand:
> SELECT setval('dna_rownum1', 1, false); -- (1)
> SELECT setval('dna_rownum2', 1, false); -- (2)
> SELECT (CASE WHEN t1.idx = t3.idx THEN t1.tag ELSE NULL END) AS tag,
I'm sorry. This one is simpler.
SELECT (CASE WHEN t1.oid = t2.idx THEN t1.tag ELSE NULL END) AS tag, t1.gb_id, t1.pos, t1.descrip FROM dna AS t1, (SELECT tag, MIN(oid) AS idx FROM dna GROUP BY tag ) AS t2WHERE t1.tag = t2.tagORDER BY t1.tag, t1.oid;
Regards,
Masaru Sugawara
