Sample script metadata

[davidonlaptop]

Write a script that downloads, clean, and normalize the metadata of all the samples information in the FTP (e.g. sample_info.txt).

Script input parameters:

• indexURL (e.g. ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.txt)

Script output (TSV Format):

• rows:
  • one row per file. Cleansed and normalized. (e.g. "-----" replaced for empty value, etc.)
• columns:
  • see the Samples tab in https://docs.google.com/spreadsheets/d/1EXe7HnYFFnJvKN9IIARDg2flwtzVTftTpHwt7f64aaI/edit#gid=0 and description in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/README_20130606_sample_info

Particular behavior

• The script should store locally on disk the original sample_info.txt. The local file's modified date should match the FTP date (for debugging).
• If the sample_info.txt has not changed since last download (file size and modified date is the same, then the script should stop executing gracefully (nothing to do).

Example

Example of how this script could be called:

./sample-metadata.sh ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_sample_info.txt   >  samples.csv