ZFIN-8631 remove GRCz11 from file name to be compliant to what jBrows…

…e expects
ZFIN · Jun 16, 2023 · a0f1643 · a0f1643
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commit a0f1643
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/server_apps/data_transfer/Downloads/GFF3/unload_mutants.sql b/server_apps/data_transfer/Downloads/GFF3/unload_mutants.sql
@@ -1,4 +1,4 @@
-\copy (select sfclg_chromosome,case when fp_prefix = 'sa' then 'ZFIN_Sanger'     when feature_type = 'TRANSGENIC_INSERTION' then 'ZFIN_transgenic'     else 'ZFIN' end as source, 'sequence_alteration' as type,sfclg_start,sfclg_end,'.', '.', '.', 'ID=' || sfclg_data_zdb_id || ';Name=' || feature_name || ';zdb_id=' || sfclg_data_zdb_id from sequence_feature_chromosome_location_generated join feature on feature_zdb_id = sfclg_data_zdb_id join feature_prefix on fp_pk_id = feature_lab_prefix_id where sfclg_data_zdb_id like 'ZDB-ALT-%'  and sfclg_assembly = 'GRCz11'  and sfclg_start is not null   and sfclg_end is not null order by 1,4,5,9 ) to 'zfin_mutants_grcz11.gff3' DELIMITER '	' ;
+\copy (select sfclg_chromosome,case when fp_prefix = 'sa' then 'ZFIN_Sanger'     when feature_type = 'TRANSGENIC_INSERTION' then 'ZFIN_transgenic'     else 'ZFIN' end as source, 'sequence_alteration' as type,sfclg_start,sfclg_end,'.', '.', '.', 'ID=' || sfclg_data_zdb_id || ';Name=' || feature_name || ';zdb_id=' || sfclg_data_zdb_id from sequence_feature_chromosome_location_generated join feature on feature_zdb_id = sfclg_data_zdb_id join feature_prefix on fp_pk_id = feature_lab_prefix_id where sfclg_data_zdb_id like 'ZDB-ALT-%'  and sfclg_assembly = 'GRCz11'  and sfclg_start is not null   and sfclg_end is not null order by 1,4,5,9 ) to 'zfin_mutants.gff3' DELIMITER '	' ;
 \copy (select sfclg_chromosome,case when fp_prefix = 'sa' then 'ZFIN_Sanger'     when feature_type = 'TRANSGENIC_INSERTION' then 'ZFIN_transgenic'     else 'ZFIN' end as source, 'sequence_alteration' as type,sfclg_start,sfclg_end,'.', '.', '.', 'ID=' || sfclg_data_zdb_id || ';Name=' || feature_name || ';zdb_id=' || sfclg_data_zdb_id from sequence_feature_chromosome_location_generated join feature on feature_zdb_id = sfclg_data_zdb_id join feature_prefix on fp_pk_id = feature_lab_prefix_id where sfclg_data_zdb_id like 'ZDB-ALT-%'  and sfclg_assembly = 'GRCz10'  and sfclg_start is not null   and sfclg_end is not null order by 1,4,5,9 ) to 'zfin_mutants_grcz10.gff3' DELIMITER '	' ;
 \copy (select sfclg_chromosome,case when fp_prefix = 'sa' then 'ZFIN_Sanger'     when feature_type = 'TRANSGENIC_INSERTION' then 'ZFIN_transgenic'     else 'ZFIN' end as source, 'sequence_alteration' as type,sfclg_start,sfclg_end,'.', '.', '.', 'ID=' || sfclg_data_zdb_id || ';Name=' || feature_name || ';zdb_id=' || sfclg_data_zdb_id from sequence_feature_chromosome_location_generated join feature on feature_zdb_id = sfclg_data_zdb_id join feature_prefix on fp_pk_id = feature_lab_prefix_id where sfclg_data_zdb_id like 'ZDB-ALT-%'  and sfclg_assembly = 'Zv9'  and sfclg_start is not null   and sfclg_end is not null order by 1,4,5,9 ) to 'zfin_mutants_zv9.gff3' DELIMITER '	' ;
 
diff --git a/server_apps/data_transfer/Downloads/GFF3/zfin_zmp_gff3.sql b/server_apps/data_transfer/Downloads/GFF3/zfin_zmp_gff3.sql
@@ -1,4 +1,4 @@
-\copy (  SELECT    sfclg_chromosome,    'ZMP',    'sequence_alteration',    sfclg_start,    sfclg_end,    '.',    '+',    '.',    'ID=' || feature_zdb_id || ';Name=' || feature_abbrev || ';zdb_id=' || feature_zdb_id || ';Alias=' || feature_zdb_id ||      ',' || feature_abbrev || ',' || feature_name  FROM sequence_feature_chromosome_location_generated  JOIN feature ON feature_zdb_id = sfclg_data_zdb_id  WHERE sfclg_assembly = 'GRCz11'  ORDER BY 1,4,5,9 ) to 'zfin_zmp_grcz11.gff3' DELIMITER '	';
+\copy (  SELECT    sfclg_chromosome,    'ZMP',    'sequence_alteration',    sfclg_start,    sfclg_end,    '.',    '+',    '.',    'ID=' || feature_zdb_id || ';Name=' || feature_abbrev || ';zdb_id=' || feature_zdb_id || ';Alias=' || feature_zdb_id ||      ',' || feature_abbrev || ',' || feature_name  FROM sequence_feature_chromosome_location_generated  JOIN feature ON feature_zdb_id = sfclg_data_zdb_id  WHERE sfclg_assembly = 'GRCz11'  ORDER BY 1,4,5,9 ) to 'zfin_zmp.gff3' DELIMITER '	';
 \copy (  SELECT    sfclg_chromosome,    'ZMP',    'sequence_alteration',    sfclg_start,    sfclg_end,    '.',    '+',    '.',    'ID=' || feature_zdb_id || ';Name=' || feature_abbrev || ';zdb_id=' || feature_zdb_id || ';Alias=' || feature_zdb_id ||      ',' || feature_abbrev || ',' || feature_name  FROM sequence_feature_chromosome_location_generated  JOIN feature ON feature_zdb_id = sfclg_data_zdb_id  WHERE sfclg_assembly = 'GRCz10'  ORDER BY 1,4,5,9 ) to 'zfin_zmp_grcz10.gff3' DELIMITER '	';
 \copy (  SELECT    sfclg_chromosome,    'ZMP',    'sequence_alteration',    sfclg_start,    sfclg_end,    '.',    '+',    '.',    'ID=' || feature_zdb_id || ';Name=' || feature_abbrev || ';zdb_id=' || feature_zdb_id || ';Alias=' || feature_zdb_id ||      ',' || feature_abbrev || ',' || feature_name  FROM sequence_feature_chromosome_location_generated  JOIN feature ON feature_zdb_id = sfclg_data_zdb_id  WHERE sfclg_assembly = 'Zv9'  ORDER BY 1,4,5,9 ) to 'zfin_zmp_zv9.gff3' DELIMITER '	';