A simple program run from the REPL for calculating average coverage of a gene from a list of genes and species
From the command line use:
java -jar target/uberjar/average-coverage-0.1.0-SNAPSHOT-standalone.jar "input_file.csv" "output_file.csv"
Expects a csv in this format (no headers):
| gene_name | species_name | length_of_fragment | percentage_coverage_of_fragment |
|---|---|---|---|
| gene_A | Homo_sapiens | 1218 | 92.34 |
| gene_A | Pan_troglodytes | 426 | 32.19 |
| gene_B | Homo_sapiens | 1071 | 100 |
| gene_B | Pan_troglodytes | 762 | 71.14 |
| gene_B | Rhinolophus_acuminatus | 204 | 19.04 |
Outputs to csv as a list of gene names with associated average percentage coverage.
Copyright © 2016 Seb Bailey