Alignment Metadata script

[davidonlaptop]

Write a script that downloads, clean, and normalize the metadata of all the alignment in the FTP (e.g. alignment.index).

Script input parameters:

• indexURL (e.g. ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/alignment.index)

Script output (TSV Format):

• rows:
  • one row per file. Cleansed and normalized. (e.g. "-----" replaced for empty value, etc.)
• columns:
  • see the BAM.Alignment tab in https://docs.google.com/spreadsheets/d/1EXe7HnYFFnJvKN9IIARDg2flwtzVTftTpHwt7f64aaI/edit#gid=0

Particular behavior

• The script should store locally on disk the original alignment.index. The local file's modified date should match the FTP date (for debugging).
• If the alignment.index 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:

./alignment-metadata.sh ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/alignment.index   >  alignments.csv