Loading script

[davidonlaptop]

Write a script that loads all data fetched from the previous scripts.

Script input parameters:

• samples
• populations
• superpopulations
• sequences
• alignments
• files

Script output (TSV Format):

• none

Particular behavior

• The script should use the database configuration file (see Database configuration file #5).
• The script should create the database if it does not exists
• The script should create the tables only if they do not exists
• If data exists, the tables should be TRUNCATED.
• One table is created for each of the 6 CSV files
• Additionally, these 2 tables are created (in-memory join mapping required):
  • sample_sequences : join table between the sequences table (for in memory join, use sample_name + fastq_filename) and the files table
  • sample_alignments : join table between the alignments table (for in memory join, use bam_filename) and the files table

Example

Example of how this script could be called:

./load-mysql.sh samples.csv populations.csv superpopulations.csv sequences.csv alignments.csv files.csv