Ensembl minimum install: Difference between revisions

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<code>perl $PS/load_seq_region.pl -coord_system_name supercontig -default_version -rank 2 -coord_system_version NCBIM37 -agp_file $HOME/workshop/genebuild/assembly/mini_supercontig_contig.agp -verbose</code>
<code>perl $PS/load_seq_region.pl -coord_system_name supercontig -default_version -rank 2 -coord_system_version NCBIM37 -agp_file $HOME/workshop/genebuild/assembly/mini_supercontig_contig.agp -verbose</code>
* See what's going on with:
* See what's going on with:
<code>select * from seq_region
  select * from seq_region
   select * from coord_system  
   select * from coord_system  
   select * from dna;</code>
   select * from dna;
* contigs:
* contigs:
<code>perl $PS/load_seq_region.pl -coord_system_name contig -default_version -rank 3 -sequence_level -coord_system_version NCBIM37 -fasta_file /home/ensembl/workshop/genebuild/assembly/clones_finished_mini.fa </code>
  perl $PS/load_seq_region.pl -coord_system_name contig -default_version -rank 3 -sequence_level -coord_system_version NCBIM37 -fasta_file /home/ensembl/workshop/genebuild/assembly/clones_finished_mini.fa </code>
* clones (only this command loads sequences into the "dna" table):
* clones (only this command loads sequences into the "dna" table):
<code>perl $PS/load_seq_region.pl $DBSPEC -coord_system_name clone -default_version -coord_system_version NCBIM37 -rank 4 -agp_file /home/ensembl/workshop/genebuild/assembly/mini_clone_contig.agp </code>
perl $PS/load_seq_region.pl $DBSPEC -coord_system_name clone -default_version -coord_system_version NCBIM37 -rank 4 -agp_file /home/ensembl/workshop/genebuild/assembly/mini_clone_contig.agp
 
* See what's going on with:
*
  select * from seq_region
  select * from coord_system
  select * from dna;
* Note that DNA sequences are not stored as a raw ASCII string in Mysql

Revision as of 12:58, 13 September 2010

Load sequences into MySQL tables

Necessary files for this example, see File:EnsemblWorkshopFiles.tar.gz

You need the fasta and AGP files for an assembly. Ensembl supports multiple coordinate systems: Any piece of DNA can be referenced by it's chromosomal location (1:1000), its super_contig location (NT_039500:1-1000) or other coordinates

Coordinate systems have a "rank" of importance (the higher the better), and a "version" (so the database contains information for several possible assemblies of the same contigs and annotations can be loaded that are based on several different versions)

  • set a little shortcut:
 export $DBSPEC="-dbhost 127.0.0.1 -dbuser ens-training -dbport 3306 -dbname mouse37_mini_ref -dbpass workshop"
  • Create an empty database named mouse37_mini_ref and populate it with the CORE schema:
 mysql -uens-training -pworkshop -h127.0.0.1 -P3306 -D mouse37_mini_ref < $HOME/cvs_checkout/ensembl/sql/table.sql
  • Load coordinates and actual sequences into the empty core database:
  • chromosome -> super_contig mappings:

perl $PS/load_seq_region.pl $DBSPEC -coord_system_name chromosome -coord_system_version NCBIM37 -rank 1 -default_version -agp_file $HOME/workshop/genebuild/assembly/mini_chr_contig.agp

  • super_contig -> contig mappings:

perl $PS/load_seq_region.pl -coord_system_name supercontig -default_version -rank 2 -coord_system_version NCBIM37 -agp_file $HOME/workshop/genebuild/assembly/mini_supercontig_contig.agp -verbose

  • See what's going on with:
 select * from seq_region
 select * from coord_system 
 select * from dna;
  • contigs:
 perl $PS/load_seq_region.pl -coord_system_name contig -default_version -rank 3 -sequence_level -coord_system_version NCBIM37 -fasta_file /home/ensembl/workshop/genebuild/assembly/clones_finished_mini.fa 
  • clones (only this command loads sequences into the "dna" table):

perl $PS/load_seq_region.pl $DBSPEC -coord_system_name clone -default_version -coord_system_version NCBIM37 -rank 4 -agp_file /home/ensembl/workshop/genebuild/assembly/mini_clone_contig.agp

  • See what's going on with:
 select * from seq_region
 select * from coord_system 
 select * from dna;
  • Note that DNA sequences are not stored as a raw ASCII string in Mysql