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average-coverage

Description

A simple program run from the REPL for calculating average coverage of a gene from a list of genes and species

Usage

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.

License

Copyright © 2016 Seb Bailey

average-coverage's People

Contributors

seb231 avatar

Stargazers

Kamil Adam avatar

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