Closed holtgrewe closed 1 year ago
Some notes on extracting sub sets for the tests.
-- meta & origin: use all uta=> set schema 'uta_20210129'; uta=> select * from gene where gene.hgnc in ('OMA1', 'OPA1'); -[ RECORD 1 ]-------------------------------------------------------- hgnc | OPA1 maploc | 3q29 descr | OPA1 mitochondrial dynamin like GTPase summary | OPA1 mitochondrial dynamin like GTPase aliases | {BERHS,MGM1,MTDPS14,NPG,NTG,largeG} added | 2014-02-10 22:59:21.153414 -[ RECORD 2 ]-------------------------------------------------------- hgnc | OMA1 maploc | 1p32.2-p32.1 descr | OMA1 zinc metallopeptidase summary | OMA1 zinc metallopeptidase aliases | {2010001O09Rik,DAB1,MPRP-1,MPRP1,YKR087C,ZMPOMA1,peptidase} added | 2014-02-10 22:59:21.153414 uta=> select * from transcript where hgnc in ('OMA1', 'OPA1'); -[ RECORD 1 ]--------------------------------- ac | NM_130831.2 origin_id | 1 hgnc | OPA1 cds_start_i | 234 cds_end_i | 3009 cds_md5 | 809b0514f1db1283c8d833512779f240 added | 2014-02-11 00:00:18.453854 -[ RECORD 2 ]--------------------------------- ac | NM_130832.2 origin_id | 1 hgnc | OPA1 cds_start_i | 234 cds_end_i | 3063 cds_md5 | 6ecdbbd7e1931c13e9846dba6f003b8f added | 2014-02-11 00:00:18.453854 [...] uta=> select * from seq_anno where ac in (select ac from transcript where hgnc in ('OMA1', 'OPA1')); -[ RECORD 1 ]---------------------------------------------------------------------------------------------------------------------------------- seq_anno_id | 198920 seq_id | 0834c1d6a05e18602acaeeade3cabd19 origin_id | 1 ac | NM_145243.4 descr | added | 2015-08-25 22:31:17.825063 -[ RECORD 2 ]---------------------------------------------------------------------------------------------------------------------------------- seq_anno_id | 78392 seq_id | 03e2faccc37f39f0ec2a39abef1858d0 origin_id | 1 ac | NM_130837.2 descr | Homo sapiens optic atrophy 1 (autosomal dominant) (OPA1), nuclear gene encoding mitochondrial protein, transcript variant 8, mRNA added | 2014-02-10 21:47:12.222509 [...] uta=> select seq_id, len from seq where sequta=> select seq_id, len from seq where seq_id in (select seq_id from seq_anno where ac in (select ac from transcript where hgnc in ('OMA1', 'OPA1'))); -[ RECORD 1 ]---------------------------- seq_id | 6f357007639453784b0ee64dd22ab84a len | 6156 -[ RECORD 2 ]---------------------------- seq_id | a45be8f1e2939958fb3b7e1dabc03556 len | 631 [...] uta=> select * from associated_accessions where tx_ac in (select ac from transcript where hgnc in ('OMA1', 'OPA1')); -[ RECORD 1 ]-----------+------------------------------ associated_accession_id | 2987826 tx_ac | NM_130832.2 pro_ac | NP_570845.1 origin | NCBI added | 2021-02-03 19:45:47.805895+00 -[ RECORD 2 ]-----------+------------------------------ associated_accession_id | 2990107 tx_ac | NM_145243.4 pro_ac | NP_660286.1 origin | NCBI added | 2021-02-03 19:45:47.805895+00 [...] uta=> select * from exon_set where tx_ac in (select ac from transcript where hgnc in ('OMA1', 'OPA1')); -[ RECORD 1 ]--+--------------------------- exon_set_id | 725664 tx_ac | NM_145243.4 alt_ac | NC_000001.10 alt_strand | -1 alt_aln_method | blat added | 2015-08-26 06:25:53.470029 -[ RECORD 2 ]--+--------------------------- exon_set_id | 371559 tx_ac | NM_145243.4 alt_ac | NC_000001.10 alt_strand | -1 alt_aln_method | splign added | 2015-08-25 23:05:15.807192 [...] uta=> select * from exon where exon_set_id in (select exon_set_id from exon_set where tx_ac in (select ac from transcript where hgnc in ('OMA1', 'OPA1'))); -[ RECORD 1 ]---------- exon_id | 2558841 exon_set_id | 257788 start_i | 193273731 end_i | 193273997 ord | 0 name | -[ RECORD 2 ]---------- exon_id | 2558842 exon_set_id | 257788 start_i | 193295335 end_i | 193295654 ord | 1 name | [...] uta=> select * from exon_aln where tx_exon_id in (select exon_id from exon where exon_set_id in (select exon_set_id from exon_set where tx_ac in (select ac from transcript where hgnc in ('OMA1', 'OPA1')))); -[ RECORD 1 ]---------------------------------------------- exon_aln_id | 6134232 tx_exon_id | 8573936 alt_exon_id | 8909645 cigar | 100= added | 2021-02-03 08:16:45.086209 tx_aseq | alt_aseq | -[ RECORD 2 ]---------------------------------------------- exon_aln_id | 6134254 tx_exon_id | 8573936 alt_exon_id | 9638401 cigar | 100= added | 2021-02-03 08:16:50.127081 tx_aseq | alt_aseq | [...]
Some notes on extracting sub sets for the tests.