Sage-Bionetworks/SMC-Het-Challenge

Name: SMC-Het-Challenge

Owner: Sage Bionetworks

Description: Development of the automated scoring system for the SMC-Het Challenge

Created: 2014-12-12 21:26:30.0

Updated: 2016-11-30 19:14:17.0

Pushed: 2017-12-14 21:48:36.0

Homepage: null

Size: 100250

Language: Python

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README

SMC-Het-Challenge

Development of the automated scoring system for the SMC-Het Challenge

Evaluator

The evaluator for the SMC-Het Challenges is the python script SMCScoring.py.

To run it, you will need to pass in the following arguments..

• -c - choose from [1A, 1B, 1C, 2A, 2B, 3A, 3B]
• –predfiles - path(s) to the prediction file(s)
• –truthfiles - path(s) to the truth file(s)
• –vcf - path to the scoring vcf file
• -o - desired path to the output file
• –approx - (OPTIONAL) triggers subsampling mode; requires 2 arguments
• sampling fraction - a float value 0.0 < x < 1.0 that denotes the sampling portion of the full matrix
• number of iterations - integer specifying number of iterations to run
• –approx_seed - (OPTIONAL) allows you to specify the seed value for the random behaviour of –approx

Examples

Running Challenge 1A

on SMCScoring.py -c 1A --predfiles ./some/path/to/1A_pred.txt --truthfiles ./some/path/to/1A_truth.txt -o ./some/path/to/1A_score.txt

Running Challenge 3A

on SMCScoring.py -c 3A --predfiles ./some/path/to/2A_pred.txt ./some/path/to/3A_pred.txt --truthfiles ./some/path/to/2A_truth.txt ./some/path/to/3A_truth.txt --vcf ./some/path/to/scoring.vcf -o ./some/path/to/3A_score.txt

Running Challenge 2B with Subsampling

on SMCScoring.py -c 2B --predfiles ./some/path/to/2B_pred.txt.gz --truthfiles ./some/path/to/2B_truth.txt.gz --vcf ./some/path/to/scoring.vcf -o ./some/path/to/2B_score.txt --approx 0.4 10